library(multiMiR)
## Welcome to multiMiR.
## 
## multiMiR database URL has been set to the 
## default value: http://multimir.org/
## 
## Database Version: 2.3.0  Updated: 2020-04-15
library(clusterProfiler)
## 
## clusterProfiler v4.12.2 Learn more at https://yulab-smu.top/contribution-knowledge-mining/
## 
## Please cite:
## 
## Guangchuang Yu, Li-Gen Wang, Yanyan Han and Qing-Yu He.
## clusterProfiler: an R package for comparing biological themes among
## gene clusters. OMICS: A Journal of Integrative Biology 2012,
## 16(5):284-287
## 
## Attaching package: 'clusterProfiler'
## The following object is masked from 'package:multiMiR':
## 
##     select
## The following object is masked from 'package:stats':
## 
##     filter
library(org.Hs.eg.db)
## Loading required package: AnnotationDbi
## Loading required package: stats4
## Loading required package: BiocGenerics
## 
## Attaching package: 'BiocGenerics'
## The following objects are masked from 'package:stats':
## 
##     IQR, mad, sd, var, xtabs
## The following objects are masked from 'package:base':
## 
##     anyDuplicated, aperm, append, as.data.frame, basename, cbind,
##     colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find,
##     get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply,
##     match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
##     Position, rank, rbind, Reduce, rownames, sapply, setdiff, table,
##     tapply, union, unique, unsplit, which.max, which.min
## Loading required package: Biobase
## Welcome to Bioconductor
## 
##     Vignettes contain introductory material; view with
##     'browseVignettes()'. To cite Bioconductor, see
##     'citation("Biobase")', and for packages 'citation("pkgname")'.
## Loading required package: IRanges
## Loading required package: S4Vectors
## 
## Attaching package: 'S4Vectors'
## The following object is masked from 'package:clusterProfiler':
## 
##     rename
## The following object is masked from 'package:utils':
## 
##     findMatches
## The following objects are masked from 'package:base':
## 
##     expand.grid, I, unname
## 
## Attaching package: 'IRanges'
## The following object is masked from 'package:clusterProfiler':
## 
##     slice
## The following object is masked from 'package:grDevices':
## 
##     windows
## 
## Attaching package: 'AnnotationDbi'
## The following object is masked from 'package:clusterProfiler':
## 
##     select
## 
library(stringr)
library(ggplot2)

0. Loading of Results

A. List of all Gene names in the dataset

gene.names = readRDS("data/derived/unique_gene_names.rds")

B. Selected Features

results.glmnet = readRDS("data/sel_features/results_glmnet_coef.rds")
sel.features = results.glmnet
sel.features
## $fold3
## $fold3$elasticnet_0.5
## $fold3$elasticnet_0.5$mse
##       (Intercept)      hsa-let-7f-1      hsa-let-7f-2      hsa-mir-106b 
##      -4.660768998      -0.602611795      -0.303241266       0.057087793 
##     hsa-mir-124-1     hsa-mir-124-3      hsa-mir-125a    hsa-mir-1270-1 
##       0.020177143       0.198244494      -0.833181786       0.196646007 
##     hsa-mir-1274b      hsa-mir-1277     hsa-mir-129-1     hsa-mir-129-2 
##       0.049593471      -0.078061541       0.015403639       0.280394056 
##      hsa-mir-1296      hsa-mir-1307      hsa-mir-130b      hsa-mir-135b 
##       0.727554050       1.321130210       0.651952177       0.214940662 
##       hsa-mir-197    hsa-mir-199a-1    hsa-mir-199a-2      hsa-mir-199b 
##       0.401597172       0.723256287       0.960442627       0.999110048 
##     hsa-mir-219-1      hsa-mir-2277      hsa-mir-3190    hsa-mir-3199-1 
##      -0.142070555      -1.028790435      -0.069032247      -0.477348224 
##    hsa-mir-320c-2       hsa-mir-326       hsa-mir-34a      hsa-mir-3647 
##      -0.147939981       0.142961419      -0.490859074      -1.274187184 
##       hsa-mir-372      hsa-mir-3909    hsa-mir-3926-1    hsa-mir-3926-2 
##       0.555923562      -0.249291482      -0.700901157      -0.193491544 
##      hsa-mir-3934       hsa-mir-425       hsa-mir-466    hsa-mir-513a-2 
##      -0.126443055       0.663266269      -0.060597443      -0.091734263 
##      hsa-mir-513b       hsa-mir-590       hsa-mir-592       hsa-mir-605 
##      -0.020343279       1.765652282      -0.340787399      -0.602116044 
##       hsa-mir-624       hsa-mir-625       hsa-mir-659       hsa-mir-664 
##      -0.006093003      -0.280042060      -1.147481063      -0.659063456 
##       hsa-mir-7-1       hsa-mir-935       MRE11A.R2Gn         ASNS.R2Gn 
##       2.240551045       0.026797327       3.652583446       0.006499477 
##         AKT1.R2Gn       CDKN1A.R2Gn        PEA15.R2Gn        MAPK1.R2Gn 
##      -1.224207246      -0.029941119       0.345050564       0.152560731 
##        STK11.R2Gn         ADAR.R2Gn        MAPK3.R2Gn       ACVRL1.R2Gn 
##      -0.413942070       0.181242058      -1.455678002       1.328790395 
##         TSC2.R2Gn         YBX1.R2Gn          JUN.R2Gn        CHEK1.R2Gn 
##      -0.090962103       0.379066706      -0.040587687       1.769312869 
##        ACACA.R2Gn       RAB11B.R2Gn        EEF2K.R2Gn       BCL2L1.R2Gn 
##       0.307049276      -0.680852733      -0.941267013      -0.358595133 
##         MSH6.R2Gn         DVL3.R2Gn       PRKAA1.R2Gn        FOXM1.R2Gn 
##       0.156468978       0.098525028      -0.085103817       0.277582923 
##        YWHAB.R2Gn          BAX.R2Gn        CASP9.R2Gn         CHGA.R2Gn 
##      -0.256142573      -1.450956141       1.037022668       2.110273941 
##         ASNS.RPPA           AR.RPPA         PDK1.RPPA         TFRC.RPPA 
##       0.238467906      -0.087821743      -0.003536870       0.039119398 
##            TP53.M          CTNNB1.M           ACACA.M              AR.M 
##       0.110847089       0.106800858       0.336451651       0.326972064 
##           MACC1.M            YAP1.g            CDH2.g             ATM.g 
##       0.318500790       0.046830810       0.168355454       0.269535559 
##           BIRC2.g          NOTCH1.g           MAPK9.g            PCNA.g 
##       0.044110774       0.222752101      -0.107384694      -0.067608748 
##           SMAD4.g           CHEK1.g            ETS1.g            NRG1.g 
##       0.005624286       0.266752753       0.416145071      -0.005731907 
##          NOTCH3.g             PGR.g           YWHAB.g           ANXA1.g 
##       0.061887757       0.045125274      -0.097228014       0.342379153 
##           SNAI2.g          SQSTM1.g  pathologic_stage pathology_T_stage 
##      -0.050136984      -0.109466127       0.222822105       0.234326716 
## 
## $fold3$elasticnet_0.5$dev
## [1] -0.836248
## 
## $fold3$elasticnet_0.5$auc
##       (Intercept)      hsa-mir-130b    hsa-mir-199a-2      hsa-mir-199b 
##      -0.685442353       0.138457472       0.157836025       0.267084550 
##       hsa-mir-592       hsa-mir-605       hsa-mir-659       hsa-mir-664 
##      -0.013872412      -0.108907656      -0.007136304      -0.466207034 
##       hsa-mir-874         AKT1.R2Gn        MAPK3.R2Gn        CHEK1.R2Gn 
##      -0.213888497      -0.158349175      -0.355740617       0.286600942 
##        FOXM1.R2Gn         XIAP.R2Gn        YWHAB.R2Gn         CHGA.R2Gn 
##       0.136249219      -0.060509423      -0.150109162       0.013014354 
##            ETS1.g  pathologic_stage pathology_T_stage 
##       0.057828320       0.061602025       0.040253755 
## 
## 
## $fold3$lasso
## $fold3$lasso$mse
## [1] -0.836248
## 
## $fold3$lasso$dev
## [1] -0.836248
## 
## $fold3$lasso$auc
##       (Intercept)     hsa-mir-129-2      hsa-mir-1296      hsa-mir-1307 
##      -7.772365251       0.249350070       0.297636812       2.165711267 
##      hsa-mir-199b      hsa-mir-2277       hsa-mir-34a      hsa-mir-3647 
##       2.534427701      -3.303359853      -0.632918567      -1.506989508 
##       hsa-mir-372    hsa-mir-3926-1       hsa-mir-590       hsa-mir-592 
##       0.314937724      -0.538248154       1.961074362      -0.180937634 
##       hsa-mir-605       hsa-mir-659       hsa-mir-664       hsa-mir-7-1 
##      -1.482319432      -2.048879451      -0.743497935       5.904715981 
##       MRE11A.R2Gn         AKT1.R2Gn       CDKN1A.R2Gn        PEA15.R2Gn 
##       7.251105049      -2.171514877      -0.003589982       0.116600148 
##        MAPK3.R2Gn       ACVRL1.R2Gn         YBX1.R2Gn        ACACA.R2Gn 
##      -1.532199694       2.205659718       0.403878951       0.094411132 
##        EEF2K.R2Gn          BAX.R2Gn        CASP9.R2Gn         CHGA.R2Gn 
##      -0.459786293      -0.688962085       0.829806982       1.423017447 
##         ASNS.RPPA           MAPK9.g            ETS1.g          SQSTM1.g 
##       0.402997745      -0.096926885       0.846511361      -0.001720483 
##  pathologic_stage pathology_T_stage 
##       0.453507516       0.516498771 
## 
## 
## 
## $fold5
## $fold5$elasticnet_0.2
## $fold5$elasticnet_0.2$mse
##       (Intercept)      hsa-mir-125a      hsa-mir-130b      hsa-mir-135b 
##      -0.729388804      -0.099991455       0.208339910       0.020981631 
##    hsa-mir-199a-1    hsa-mir-199a-2      hsa-mir-199b      hsa-mir-301b 
##       0.069947190       0.135626718       0.165027428       0.001946579 
##    hsa-mir-3199-1    hsa-mir-320c-2      hsa-mir-3647       hsa-mir-375 
##      -0.026893312      -0.013265213      -0.046192039       0.019290454 
##    hsa-mir-3926-1    hsa-mir-513a-2      hsa-mir-513b       hsa-mir-592 
##      -0.029982927      -0.005863953      -0.030460309      -0.028134603 
##       hsa-mir-605       hsa-mir-659       hsa-mir-664       hsa-mir-7-1 
##      -0.065945710      -0.059787649      -0.284682008       0.031836392 
##       hsa-mir-874         AKT1.R2Gn        MAPK9.R2Gn        MAPK3.R2Gn 
##      -0.167594900      -0.106040395      -0.040020064      -0.232456337 
##         YBX1.R2Gn        CHEK1.R2Gn        EEF2K.R2Gn       PIK3R1.R2Gn 
##       0.040764783       0.276563583      -0.019407616      -0.007220953 
##         MSH6.R2Gn       PRKAA1.R2Gn        FOXM1.R2Gn         XIAP.R2Gn 
##       0.030037995      -0.071369713       0.124833138      -0.120311109 
##        YWHAB.R2Gn        CASP9.R2Gn         CHGA.R2Gn         TFRC.RPPA 
##      -0.101335719       0.022107296       0.078646434       0.007688925 
##             ATM.g           CHEK1.g            ETS1.g  pathologic_stage 
##       0.003317895       0.003326216       0.052918061       0.045829425 
## pathology_T_stage 
##       0.039570767 
## 
## $fold5$elasticnet_0.2$dev
## [1] -0.836248
## 
## 
## $fold5$elasticnet_0.5
## $fold5$elasticnet_0.5$mse
## [1] -0.836248
## 
## $fold5$elasticnet_0.5$dev
## [1] -0.836248
## 
## 
## $fold5$lasso
## $fold5$lasso$mse
##      (Intercept)     hsa-mir-199b      hsa-mir-605      hsa-mir-664 
##      -0.28870711       0.19679922      -0.04621114      -0.83213040 
##      hsa-mir-874        AKT1.R2Gn       MAPK3.R2Gn       FOXM1.R2Gn 
##      -0.07909123      -0.02640800      -0.04602342       0.17434211 
##       YWHAB.R2Gn pathologic_stage 
##      -0.10674757       0.01222499 
## 
## $fold5$lasso$dev
## [1] -0.836248
## 
## 
## 
## $fold10
## $fold10$elasticnet_0.2
## $fold10$elasticnet_0.2$mse
##       (Intercept)      hsa-let-7f-1      hsa-let-7f-2      hsa-mir-106b 
##     -1.2750044217     -0.1056454914     -0.0090813262      0.0601083761 
##      hsa-mir-125a      hsa-mir-1277     hsa-mir-129-2      hsa-mir-1296 
##     -0.2263778959     -0.0212167741      0.0457795202      0.0551724575 
##      hsa-mir-1307      hsa-mir-130b      hsa-mir-135b       hsa-mir-197 
##      0.1030818016      0.3216261162      0.0515951496      0.1038543594 
##    hsa-mir-199a-1    hsa-mir-199a-2      hsa-mir-199b      hsa-mir-2277 
##      0.1914084203      0.2622218130      0.2883555459     -0.0464732715 
##      hsa-mir-301b    hsa-mir-3199-1    hsa-mir-320c-2       hsa-mir-34a 
##      0.0380535602     -0.1072952887     -0.0502123191     -0.0637601109 
##      hsa-mir-3647      hsa-mir-3655       hsa-mir-372       hsa-mir-375 
##     -0.2402346877     -0.0163688558      0.0144356750      0.0546170083 
##    hsa-mir-3926-1    hsa-mir-3926-2      hsa-mir-3934       hsa-mir-425 
##     -0.1133039404     -0.0041870552     -0.0002702772      0.0221976574 
##    hsa-mir-513a-2      hsa-mir-513b       hsa-mir-590       hsa-mir-592 
##     -0.0212232388     -0.0401509369      0.1542697766     -0.0786273589 
##       hsa-mir-605       hsa-mir-653       hsa-mir-659       hsa-mir-664 
##     -0.1151543057     -0.0042918627     -0.1827203270     -0.3256797411 
##       hsa-mir-7-1       hsa-mir-874       MRE11A.R2Gn         AKT1.R2Gn 
##      0.2626847423     -0.1634560743      0.4243082228     -0.2277108477 
##        PEA15.R2Gn        MAPK9.R2Gn        MAPK3.R2Gn       ACVRL1.R2Gn 
##      0.0322865993     -0.0359925563     -0.4121256152      0.0423359102 
##         TSC2.R2Gn         YBX1.R2Gn        CHEK1.R2Gn        EEF2K.R2Gn 
##     -0.0453683245      0.1078556421      0.4101582817     -0.1456199392 
##       PIK3R1.R2Gn         MSH6.R2Gn       PRKAA1.R2Gn        FOXM1.R2Gn 
##     -0.0123974856      0.1030376901     -0.1645600451      0.1538144507 
##         XIAP.R2Gn        YWHAB.R2Gn        CASP9.R2Gn         CHGA.R2Gn 
##     -0.1147957225     -0.1307486700      0.1564407940      0.2820661029 
##         ASNS.RPPA         TFRC.RPPA            YAP1.g             ATM.g 
##      0.0461333900      0.0200968227      0.0104253976      0.0497608041 
##           BIRC2.g           MAPK9.g            PCNA.g           CHEK1.g 
##      0.0103757012     -0.0015915140     -0.0202581363      0.0497075363 
##            ETS1.g          NOTCH3.g             PGR.g           YWHAB.g 
##      0.1003490714      0.0140747310      0.0103385272     -0.0247295849 
##           ANXA1.g          SQSTM1.g  pathologic_stage pathology_T_stage 
##      0.0463202334     -0.0015961411      0.0736597452      0.0630713941 
## 
## $fold10$elasticnet_0.2$dev
##       (Intercept)      hsa-let-7f-1      hsa-let-7f-2      hsa-mir-106b 
##      -1.363746577      -0.127144193      -0.026490410       0.075048015 
##      hsa-mir-125a      hsa-mir-1277     hsa-mir-129-1     hsa-mir-129-2 
##      -0.245703678      -0.046748076       0.001451632       0.055730284 
##      hsa-mir-1296      hsa-mir-1307      hsa-mir-130b      hsa-mir-135b 
##       0.075081609       0.124486937       0.334503327       0.056214936 
##       hsa-mir-197    hsa-mir-199a-1    hsa-mir-199a-2      hsa-mir-199b 
##       0.118884777       0.211574535       0.282681944       0.308071197 
##      hsa-mir-2277      hsa-mir-301b    hsa-mir-3199-1    hsa-mir-320c-2 
##      -0.082137182       0.042840992      -0.117823756      -0.055784909 
##       hsa-mir-34a      hsa-mir-3647      hsa-mir-3655       hsa-mir-372 
##      -0.075383660      -0.270732618      -0.019625419       0.028592680 
##       hsa-mir-375      hsa-mir-3909    hsa-mir-3926-1    hsa-mir-3926-2 
##       0.055255984      -0.005084634      -0.128279940      -0.010910663 
##      hsa-mir-3934       hsa-mir-425    hsa-mir-513a-2      hsa-mir-513b 
##      -0.006456341       0.049816877      -0.023006509      -0.040409771 
##       hsa-mir-590       hsa-mir-592       hsa-mir-605       hsa-mir-653 
##       0.201359436      -0.085398714      -0.122868934      -0.010428513 
##       hsa-mir-659       hsa-mir-664       hsa-mir-7-1       hsa-mir-874 
##      -0.205177074      -0.326969171       0.303567612      -0.157678411 
##       MRE11A.R2Gn         AKT1.R2Gn        PEA15.R2Gn        MAPK9.R2Gn 
##       0.523315672      -0.247893660       0.043995877      -0.031312139 
##        MAPK3.R2Gn       ACVRL1.R2Gn         TSC2.R2Gn         YBX1.R2Gn 
##      -0.441914231       0.069915393      -0.066973081       0.113820793 
##        CHEK1.R2Gn        EEF2K.R2Gn       PIK3R1.R2Gn       BCL2L1.R2Gn 
##       0.435355653      -0.163094953      -0.012036551      -0.007923252 
##         MSH6.R2Gn       PRKAA1.R2Gn        FOXM1.R2Gn         XIAP.R2Gn 
##       0.111081465      -0.172967037       0.157593371      -0.103494146 
##        YWHAB.R2Gn          BAX.R2Gn         TFRC.R2Gn        CASP9.R2Gn 
##      -0.135707193      -0.039130371       0.001506770       0.174146802 
##         CHGA.R2Gn         ASNS.RPPA           AR.RPPA         TFRC.RPPA 
##       0.321811489       0.054882397      -0.006117451       0.021768195 
##            YAP1.g             ATM.g           BIRC2.g           MAPK9.g 
##       0.014848084       0.056527391       0.014802137      -0.005117267 
##            PCNA.g           CHEK1.g            ETS1.g          NOTCH3.g 
##      -0.023507077       0.056490344       0.107042339       0.019275337 
##             PGR.g           YWHAB.g           ANXA1.g          SQSTM1.g 
##       0.014770020      -0.030320819       0.059024427      -0.005125231 
##  pathologic_stage pathology_T_stage 
##       0.076774845       0.066523877 
## 
## 
## $fold10$elasticnet_0.5
## $fold10$elasticnet_0.5$mse
## [1] -0.836248
## 
## $fold10$elasticnet_0.5$dev
## [1] -0.836248
## 
## 
## $fold10$lasso
## $fold10$lasso$mse
## [1] -0.836248
## 
## $fold10$lasso$dev
## [1] -0.836248

1. Convert microRNA to genes

Also remove the ending “.R2Gn” and “.RPPA” from gene names.

split.by.omic = function(variable.list) {
  out.mRSG = variable.list[startsWith(variable.list, "hsa")]
  out.R2Gn = variable.list[endsWith(variable.list, ".R2Gn")]
  out.RPPA = variable.list[endsWith(variable.list, ".RPPA")]
  #Mutations and gistict for glmnet only
  out.M = variable.list[endsWith(variable.list, ".M")] 
  out.g = variable.list[endsWith(variable.list, ".g")] 
  out = list("miRNASeqGene" = out.mRSG,
             "RNASeq2GeneNorm" = out.R2Gn,
             "RPPAArray" = out.RPPA,
             "Mutations" = out.M,
             "gistict" = out.g)
  out
}
multiomics.to.GENES = function(sel.features, full.search = F, table = "validated", drop.miRNA = F) {
  multiomics.list = split.by.omic(sel.features)
  # Convert miRNASeqGene to target GENE names
  # Skipped and returns an empty list instead of the list of select features,
  # or if microRNA features are explicitly dropped (drop.miRNA = T).
  # (Usually done when the features has only a few miRNA and unable to target any genes)
  if (length(multiomics.list[[1]]) > 0 & !drop.miRNA) {
    if (!full.search) { # Search only among the 198 genes in ACC, recommended
    targets= get_multimir(mirna = multiomics.list[[1]], 
                          target = gene.names,
                          table = table,
                          summary = T)
    mRSG.target.genes = unique(targets@data$target_symbol)
    } else { # Search the full dataset, not recommended. 
             # Use only if ACC gene search returns nothing or fails.
             # Genes not in the ACC genes need to be manually removed.
    targets= get_multimir(mirna = multiomics.list[[1]], 
                          table = table,
                          summary = T)  
    mRSG.target.genes = unique(targets@data$target_symbol)
    }
    
  } else {
    mRSG.target.genes = list()
  }
  #Remove suffix for Pathway Analysis Compatibility
  R2Gn.genes = str_remove(multiomics.list[[2]], ".R2Gn")
  
  RPPA.genes = str_remove(multiomics.list[[3]], ".RPPA")
  
  M.genes = str_remove(multiomics.list[[4]], ".M")
  
  g.genes = str_remove(multiomics.list[[5]], ".g")
  
  #Join all cleaned-up genes are remove duplicates.
  out1 = c(mRSG.target.genes, R2Gn.genes, RPPA.genes, M.genes, g.genes)
  out = as.character(unique(out1))
  out
}
geneNames <- list("3F_0.5_MSE"=multiomics.to.GENES(names(sel.features$fold3$elasticnet_0.5$mse)),
                  "3F_0.5_AUC"=multiomics.to.GENES(names(sel.features$fold3$elasticnet_0.5$auc)),
                  "3F_1_AUC"=multiomics.to.GENES(names(sel.features$fold3$lasso$auc)),
                  "5F_0.2_MSE"=multiomics.to.GENES(names(sel.features$fold5$elasticnet_0.2$mse)),
                  "5F_1_MSE"=multiomics.to.GENES(names(sel.features$fold5$lasso$mse), drop.miRNA = T ), # 4 microRNAs dropped
                  "10F_0.2_MSE"=multiomics.to.GENES(names(sel.features$fold10$elasticnet_0.2$mse)),
                  "10F_0.2_DEV"=multiomics.to.GENES(names(sel.features$fold10$elasticnet_0.2$dev)))
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geneNames
## $`3F_0.5_MSE`
##  [1] "NOTCH1"  "ERBB2"   "NF2"     "KRAS"    "CCND1"   "AKT1"    "BCL2L1" 
##  [8] "AR"      "FASN"    "RB1"     "PIK3R1"  "XIAP"    "CHEK1"   "IGF1R"  
## [15] "SRSF1"   "TUBA1B"  "CDK1"    "YBX1"    "BECN1"   "ERBB3"   "FOXO3"  
## [22] "ACACA"   "E2F1"    "MYC"     "BCL2L11" "RAF1"    "XBP1"    "AKT3"   
## [29] "EEF2"    "EIF4G1"  "GSK3B"   "MSH6"    "ITGA2"   "KDR"     "MRE11A" 
## [36] "ASNS"    "CDKN1A"  "PEA15"   "MAPK1"   "STK11"   "ADAR"    "MAPK3"  
## [43] "ACVRL1"  "TSC2"    "JUN"     "RAB11B"  "EEF2K"   "DVL3"    "PRKAA1" 
## [50] "FOXM1"   "YWHAB"   "BAX"     "CASP9"   "CHGA"    "PDK1"    "TFRC"   
## [57] "TP53"    "CTNNB1"  "MACC1"   "YAP1"    "CDH2"    "ATM"     "BIRC2"  
## [64] "MAPK9"   "PCNA"    "SMAD4"   "ETS1"    "NRG1"    "NOTCH3"  "PGR"    
## [71] "ANXA1"   "SNAI2"   "SQSTM1" 
## 
## $`3F_0.5_AUC`
##  [1] "ERBB3"  "FOXO3"  "IGF1R"  "ACACA"  "CCND1"  "MYC"    "EIF4G1" "AKT1"  
##  [9] "MAPK3"  "CHEK1"  "FOXM1"  "XIAP"   "YWHAB"  "CHGA"   "ETS1"  
## 
## $`3F_1_AUC`
##  [1] "ERBB3"  "FOXO3"  "IGF1R"  "ACACA"  "CCND1"  "MYC"    "EIF4G1" "MRE11A"
##  [9] "AKT1"   "CDKN1A" "PEA15"  "MAPK3"  "ACVRL1" "YBX1"   "EEF2K"  "BAX"   
## [17] "CASP9"  "CHGA"   "ASNS"   "MAPK9"  "ETS1"   "SQSTM1"
## 
## $`5F_0.2_MSE`
##  [1] "ERBB3"   "FOXO3"   "IGF1R"   "ACACA"   "BCL2"    "ERBB2"   "AXL"    
##  [8] "BAK1"    "MYC"     "CASP3"   "BCL2L11" "TP53"    "YAP1"    "YWHAZ"  
## [15] "STAT3"   "PARP1"   "XIAP"    "CTNNB1"  "PRDX1"   "PDK1"    "PIK3CA" 
## [22] "PRKCA"   "MAPK3"   "TFRC"    "TGM2"    "CCND1"   "EIF4G1"  "MYH9"   
## [29] "CDKN1A"  "IRS1"    "JUN"     "RAF1"    "TYMS"    "ANXA7"   "CLDN7"  
## [36] "CTNNA1"  "YBX1"    "RPS6"    "SRSF1"   "NDRG1"   "PECAM1"  "YWHAB"  
## [43] "SETD2"   "AKT1"    "MAPK9"   "CHEK1"   "EEF2K"   "PIK3R1"  "MSH6"   
## [50] "PRKAA1"  "FOXM1"   "CASP9"   "CHGA"    "ATM"     "ETS1"   
## 
## $`5F_1_MSE`
## [1] "AKT1"  "MAPK3" "FOXM1" "YWHAB"
## 
## $`10F_0.2_MSE`
##  [1] "ERBB3"   "FOXO3"   "IGF1R"   "ACACA"   "BCL2"    "ERBB2"   "AXL"    
##  [8] "BAK1"    "MYC"     "CASP3"   "BCL2L11" "TP53"    "YAP1"    "YWHAZ"  
## [15] "STAT3"   "PARP1"   "XIAP"    "CTNNB1"  "PRDX1"   "PDK1"    "PIK3CA" 
## [22] "PRKCA"   "MAPK3"   "TFRC"    "TGM2"    "MYH9"    "CCND1"   "CDKN1A" 
## [29] "IRS1"    "JUN"     "RAF1"    "TYMS"    "ANXA7"   "CLDN7"   "CTNNA1" 
## [36] "EIF4G1"  "YBX1"    "RPS6"    "SRSF1"   "NDRG1"   "PECAM1"  "YWHAB"  
## [43] "SETD2"   "MRE11A"  "AKT1"    "PEA15"   "MAPK9"   "ACVRL1"  "TSC2"   
## [50] "CHEK1"   "EEF2K"   "PIK3R1"  "MSH6"    "PRKAA1"  "FOXM1"   "CASP9"  
## [57] "CHGA"    "ASNS"    "ATM"     "BIRC2"   "PCNA"    "ETS1"    "NOTCH3" 
## [64] "PGR"     "ANXA1"   "SQSTM1" 
## 
## $`10F_0.2_DEV`
##  [1] "RB1"     "ERBB3"   "FOXO3"   "IGF1R"   "ACACA"   "BCL2"    "ERBB2"  
##  [8] "AXL"     "BAK1"    "MYC"     "CASP3"   "BCL2L11" "TP53"    "YAP1"   
## [15] "YWHAZ"   "STAT3"   "PARP1"   "XIAP"    "CTNNB1"  "PRDX1"   "PDK1"   
## [22] "PIK3CA"  "PRKCA"   "MAPK3"   "TFRC"    "TGM2"    "MYH9"    "CCND1"  
## [29] "CDKN1A"  "IRS1"    "JUN"     "RAF1"    "TYMS"    "ANXA7"   "CLDN7"  
## [36] "CTNNA1"  "EIF4G1"  "YBX1"    "RPS6"    "SRSF1"   "NDRG1"   "PECAM1" 
## [43] "YWHAB"   "SETD2"   "MRE11A"  "AKT1"    "PEA15"   "MAPK9"   "ACVRL1" 
## [50] "TSC2"    "CHEK1"   "EEF2K"   "PIK3R1"  "BCL2L1"  "MSH6"    "PRKAA1" 
## [57] "FOXM1"   "BAX"     "CASP9"   "CHGA"    "ASNS"    "AR"      "ATM"    
## [64] "BIRC2"   "PCNA"    "ETS1"    "NOTCH3"  "PGR"     "ANXA1"   "SQSTM1"
saveRDS(geneNames, file = "data/sel_features/gene_converted/genes_glmnet.rds")

2. Pathway Analysis

A. GO Classification

ggo_MF <- list()#functional profile of a geneset for Molecular Function
ggo_BP <- list()#functional profile of a geneset for Biological Process
ggo_CC <- list()#functional profile of a geneset for Cellular Component


for(z in 1:length(geneNames)){
  print(z)
  input <- geneNames[[z]]

  ggo_MF[[z]] <- groupGO(gene=input,
    OrgDb = org.Hs.eg.db,
    ont="MF",
    keyType="SYMBOL",
    readable=TRUE)
  
  ggo_BP[[z]] <- groupGO(gene=input,
    OrgDb = org.Hs.eg.db,
    ont="BP",
    keyType="SYMBOL",
    readable=TRUE)

  ggo_CC[[z]] <- groupGO(gene=input,
    OrgDb = org.Hs.eg.db,
    ont="CC",
    keyType="SYMBOL",
    readable=TRUE)    
}
## [1] 1
## [1] 2
## [1] 3
## [1] 4
## [1] 5
## [1] 6
## [1] 7
for(z in 1:length(geneNames)) {
  print(head(ggo_MF[[z]]))
  print(head(ggo_BP[[z]]))
  print(head(ggo_CC[[z]]))
}
##                    ID                  Description Count GeneRatio
## GO:0003774 GO:0003774  cytoskeletal motor activity     0      0/73
## GO:0003824 GO:0003824           catalytic activity    34     34/73
## GO:0005198 GO:0005198 structural molecule activity     1      1/73
## GO:0005215 GO:0005215         transporter activity     2      2/73
## GO:0005488 GO:0005488                      binding    71     71/73
## GO:0009055 GO:0009055   electron transfer activity     0      0/73
##                                                                                                                                                                                                                                                                                                                                                                                                                  geneID
## GO:0003774                                                                                                                                                                                                                                                                                                                                                                                                             
## GO:0003824                                                                                                                                                                                                             ERBB2/KRAS/CCND1/AKT1/FASN/PIK3R1/XIAP/CHEK1/IGF1R/TUBA1B/CDK1/ACACA/RAF1/AKT3/EEF2/GSK3B/MSH6/KDR/ASNS/CDKN1A/MAPK1/STK11/ADAR/MAPK3/ACVRL1/RAB11B/EEF2K/PRKAA1/CASP9/PDK1/ATM/BIRC2/MAPK9/PCNA
## GO:0005198                                                                                                                                                                                                                                                                                                                                                                                                       TUBA1B
## GO:0005215                                                                                                                                                                                                                                                                                                                                                                                                    IGF1R/BAX
## GO:0005488 NOTCH1/ERBB2/NF2/KRAS/CCND1/AKT1/BCL2L1/AR/FASN/RB1/PIK3R1/XIAP/CHEK1/IGF1R/SRSF1/TUBA1B/CDK1/YBX1/BECN1/ERBB3/FOXO3/ACACA/E2F1/MYC/BCL2L11/RAF1/XBP1/AKT3/EEF2/EIF4G1/GSK3B/MSH6/ITGA2/KDR/ASNS/CDKN1A/PEA15/MAPK1/STK11/ADAR/MAPK3/ACVRL1/TSC2/JUN/RAB11B/EEF2K/DVL3/PRKAA1/FOXM1/YWHAB/BAX/CASP9/PDK1/TFRC/TP53/CTNNB1/MACC1/YAP1/CDH2/ATM/BIRC2/MAPK9/PCNA/SMAD4/ETS1/NRG1/NOTCH3/PGR/ANXA1/SNAI2/SQSTM1
## GO:0009055                                                                                                                                                                                                                                                                                                                                                                                                             
##                    ID           Description Count GeneRatio
## GO:0000003 GO:0000003          reproduction    19     19/73
## GO:0002376 GO:0002376 immune system process    32     32/73
## GO:0008152 GO:0008152     metabolic process    66     66/73
## GO:0009987 GO:0009987      cellular process    72     72/73
## GO:0016032 GO:0016032         viral process    10     10/73
## GO:0022414 GO:0022414  reproductive process    19     19/73
##                                                                                                                                                                                                                                                                                                                                                                                                                       geneID
## GO:0000003                                                                                                                                                                                                                                                                                                             NOTCH1/AKT1/BCL2L1/AR/RB1/IGF1R/CDK1/FOXO3/BCL2L11/MSH6/ITGA2/KDR/STK11/BAX/CTNNB1/ATM/PCNA/SMAD4/PGR
## GO:0002376                                                                                                                                                                                                                              NOTCH1/ERBB2/AKT1/RB1/PIK3R1/XIAP/IGF1R/BECN1/FOXO3/MYC/BCL2L11/RAF1/XBP1/MSH6/ITGA2/CDKN1A/MAPK1/STK11/ADAR/MAPK3/BAX/CHGA/TFRC/TP53/CTNNB1/ATM/BIRC2/MAPK9/ETS1/ANXA1/SNAI2/SQSTM1
## GO:0008152                                       NOTCH1/ERBB2/NF2/KRAS/CCND1/AKT1/AR/FASN/RB1/PIK3R1/XIAP/CHEK1/IGF1R/SRSF1/CDK1/YBX1/BECN1/ERBB3/FOXO3/ACACA/E2F1/MYC/RAF1/XBP1/AKT3/EEF2/EIF4G1/GSK3B/MSH6/ITGA2/KDR/ASNS/CDKN1A/MAPK1/STK11/ADAR/MAPK3/ACVRL1/TSC2/JUN/RAB11B/EEF2K/DVL3/PRKAA1/FOXM1/YWHAB/BAX/CASP9/PDK1/TFRC/TP53/CTNNB1/MACC1/YAP1/ATM/BIRC2/MAPK9/PCNA/SMAD4/ETS1/NRG1/NOTCH3/PGR/ANXA1/SNAI2/SQSTM1
## GO:0009987 NOTCH1/ERBB2/NF2/KRAS/CCND1/AKT1/BCL2L1/AR/FASN/RB1/PIK3R1/XIAP/CHEK1/IGF1R/SRSF1/TUBA1B/CDK1/YBX1/BECN1/ERBB3/FOXO3/ACACA/E2F1/MYC/BCL2L11/RAF1/XBP1/AKT3/EEF2/EIF4G1/GSK3B/MSH6/ITGA2/KDR/ASNS/CDKN1A/PEA15/MAPK1/STK11/ADAR/MAPK3/ACVRL1/TSC2/JUN/RAB11B/EEF2K/DVL3/PRKAA1/FOXM1/YWHAB/BAX/CASP9/CHGA/PDK1/TFRC/TP53/CTNNB1/MACC1/YAP1/CDH2/ATM/BIRC2/MAPK9/PCNA/SMAD4/ETS1/NRG1/NOTCH3/PGR/ANXA1/SNAI2/SQSTM1
## GO:0016032                                                                                                                                                                                                                                                                                                                                                             NOTCH1/AKT1/CDK1/BECN1/GSK3B/ITGA2/ADAR/JUN/TFRC/TP53
## GO:0022414                                                                                                                                                                                                                                                                                                             NOTCH1/AKT1/BCL2L1/AR/RB1/IGF1R/CDK1/FOXO3/BCL2L11/MSH6/ITGA2/KDR/STK11/BAX/CTNNB1/ATM/PCNA/SMAD4/PGR
##                    ID                Description Count GeneRatio
## GO:0032991 GO:0032991 protein-containing complex    52     52/73
## GO:0044423 GO:0044423           virion component     0      0/73
## GO:0110165 GO:0110165 cellular anatomical entity    72     72/73
##                                                                                                                                                                                                                                                                                                                                                                                                                       geneID
## GO:0032991                                                                                                                  NOTCH1/ERBB2/CCND1/AKT1/BCL2L1/AR/RB1/PIK3R1/CHEK1/IGF1R/SRSF1/CDK1/YBX1/BECN1/ERBB3/FOXO3/E2F1/MYC/BCL2L11/XBP1/EEF2/EIF4G1/GSK3B/MSH6/ITGA2/KDR/CDKN1A/PEA15/STK11/ADAR/ACVRL1/TSC2/JUN/DVL3/PRKAA1/FOXM1/BAX/CASP9/PDK1/TFRC/TP53/CTNNB1/YAP1/CDH2/ATM/BIRC2/PCNA/SMAD4/ETS1/NOTCH3/PGR/SNAI2
## GO:0044423                                                                                                                                                                                                                                                                                                                                                                                                                  
## GO:0110165 NOTCH1/ERBB2/NF2/KRAS/CCND1/AKT1/BCL2L1/AR/FASN/RB1/PIK3R1/XIAP/CHEK1/IGF1R/SRSF1/TUBA1B/CDK1/YBX1/BECN1/ERBB3/FOXO3/ACACA/E2F1/MYC/BCL2L11/RAF1/XBP1/AKT3/EEF2/EIF4G1/GSK3B/MSH6/ITGA2/KDR/ASNS/CDKN1A/PEA15/MAPK1/STK11/ADAR/MAPK3/ACVRL1/TSC2/JUN/RAB11B/EEF2K/DVL3/PRKAA1/FOXM1/YWHAB/BAX/CASP9/CHGA/PDK1/TFRC/TP53/CTNNB1/MACC1/YAP1/CDH2/ATM/BIRC2/MAPK9/PCNA/SMAD4/ETS1/NRG1/NOTCH3/PGR/ANXA1/SNAI2/SQSTM1
##                    ID                  Description Count GeneRatio
## GO:0003774 GO:0003774  cytoskeletal motor activity     0      0/15
## GO:0003824 GO:0003824           catalytic activity     7      7/15
## GO:0005198 GO:0005198 structural molecule activity     0      0/15
## GO:0005215 GO:0005215         transporter activity     1      1/15
## GO:0005488 GO:0005488                      binding    14     14/15
## GO:0009055 GO:0009055   electron transfer activity     0      0/15
##                                                                                     geneID
## GO:0003774                                                                                
## GO:0003824                                         IGF1R/ACACA/CCND1/AKT1/MAPK3/CHEK1/XIAP
## GO:0005198                                                                                
## GO:0005215                                                                           IGF1R
## GO:0005488 ERBB3/FOXO3/IGF1R/ACACA/CCND1/MYC/EIF4G1/AKT1/MAPK3/CHEK1/FOXM1/XIAP/YWHAB/ETS1
## GO:0009055                                                                                
##                    ID           Description Count GeneRatio
## GO:0000003 GO:0000003          reproduction     3      3/15
## GO:0002376 GO:0002376 immune system process     8      8/15
## GO:0008152 GO:0008152     metabolic process    14     14/15
## GO:0009987 GO:0009987      cellular process    15     15/15
## GO:0016032 GO:0016032         viral process     1      1/15
## GO:0022414 GO:0022414  reproductive process     3      3/15
##                                                                                          geneID
## GO:0000003                                                                     FOXO3/IGF1R/AKT1
## GO:0002376                                            FOXO3/IGF1R/MYC/AKT1/MAPK3/XIAP/CHGA/ETS1
## GO:0008152      ERBB3/FOXO3/IGF1R/ACACA/CCND1/MYC/EIF4G1/AKT1/MAPK3/CHEK1/FOXM1/XIAP/YWHAB/ETS1
## GO:0009987 ERBB3/FOXO3/IGF1R/ACACA/CCND1/MYC/EIF4G1/AKT1/MAPK3/CHEK1/FOXM1/XIAP/YWHAB/CHGA/ETS1
## GO:0016032                                                                                 AKT1
## GO:0022414                                                                     FOXO3/IGF1R/AKT1
##                    ID                Description Count GeneRatio
## GO:0032991 GO:0032991 protein-containing complex    10     10/15
## GO:0044423 GO:0044423           virion component     0      0/15
## GO:0110165 GO:0110165 cellular anatomical entity    15     15/15
##                                                                                          geneID
## GO:0032991                             ERBB3/FOXO3/IGF1R/CCND1/MYC/EIF4G1/AKT1/CHEK1/FOXM1/ETS1
## GO:0044423                                                                                     
## GO:0110165 ERBB3/FOXO3/IGF1R/ACACA/CCND1/MYC/EIF4G1/AKT1/MAPK3/CHEK1/FOXM1/XIAP/YWHAB/CHGA/ETS1
##                    ID                  Description Count GeneRatio
## GO:0003774 GO:0003774  cytoskeletal motor activity     0      0/22
## GO:0003824 GO:0003824           catalytic activity    11     11/22
## GO:0005198 GO:0005198 structural molecule activity     0      0/22
## GO:0005215 GO:0005215         transporter activity     2      2/22
## GO:0005488 GO:0005488                      binding    20     20/22
## GO:0009055 GO:0009055   electron transfer activity     0      0/22
##                                                                                                                         geneID
## GO:0003774                                                                                                                    
## GO:0003824                                                   IGF1R/ACACA/CCND1/AKT1/CDKN1A/MAPK3/ACVRL1/EEF2K/CASP9/ASNS/MAPK9
## GO:0005198                                                                                                                    
## GO:0005215                                                                                                           IGF1R/BAX
## GO:0005488 ERBB3/FOXO3/IGF1R/ACACA/CCND1/MYC/EIF4G1/AKT1/CDKN1A/PEA15/MAPK3/ACVRL1/YBX1/EEF2K/BAX/CASP9/ASNS/MAPK9/ETS1/SQSTM1
## GO:0009055                                                                                                                    
##                    ID           Description Count GeneRatio
## GO:0000003 GO:0000003          reproduction     4      4/22
## GO:0002376 GO:0002376 immune system process    11     11/22
## GO:0008152 GO:0008152     metabolic process    19     19/22
## GO:0009987 GO:0009987      cellular process    21     21/22
## GO:0016032 GO:0016032         viral process     1      1/22
## GO:0022414 GO:0022414  reproductive process     4      4/22
##                                                                                                                              geneID
## GO:0000003                                                                                                     FOXO3/IGF1R/AKT1/BAX
## GO:0002376                                                             FOXO3/IGF1R/MYC/AKT1/CDKN1A/MAPK3/BAX/CHGA/MAPK9/ETS1/SQSTM1
## GO:0008152            ERBB3/FOXO3/IGF1R/ACACA/CCND1/MYC/EIF4G1/AKT1/CDKN1A/MAPK3/ACVRL1/YBX1/EEF2K/BAX/CASP9/ASNS/MAPK9/ETS1/SQSTM1
## GO:0009987 ERBB3/FOXO3/IGF1R/ACACA/CCND1/MYC/EIF4G1/AKT1/CDKN1A/PEA15/MAPK3/ACVRL1/YBX1/EEF2K/BAX/CASP9/CHGA/ASNS/MAPK9/ETS1/SQSTM1
## GO:0016032                                                                                                                     AKT1
## GO:0022414                                                                                                     FOXO3/IGF1R/AKT1/BAX
##                    ID                Description Count GeneRatio
## GO:0032991 GO:0032991 protein-containing complex    14     14/22
## GO:0044423 GO:0044423           virion component     0      0/22
## GO:0110165 GO:0110165 cellular anatomical entity    21     21/22
##                                                                                                                              geneID
## GO:0032991                                          ERBB3/FOXO3/IGF1R/CCND1/MYC/EIF4G1/AKT1/CDKN1A/PEA15/ACVRL1/YBX1/BAX/CASP9/ETS1
## GO:0044423                                                                                                                         
## GO:0110165 ERBB3/FOXO3/IGF1R/ACACA/CCND1/MYC/EIF4G1/AKT1/CDKN1A/PEA15/MAPK3/ACVRL1/YBX1/EEF2K/BAX/CASP9/CHGA/ASNS/MAPK9/ETS1/SQSTM1
##                    ID                  Description Count GeneRatio
## GO:0003774 GO:0003774  cytoskeletal motor activity     1      1/55
## GO:0003824 GO:0003824           catalytic activity    27     27/55
## GO:0005198 GO:0005198 structural molecule activity     3      3/55
## GO:0005215 GO:0005215         transporter activity     3      3/55
## GO:0005488 GO:0005488                      binding    54     54/55
## GO:0009055 GO:0009055   electron transfer activity     0      0/55
##                                                                                                                                                                                                                                                                                                                          geneID
## GO:0003774                                                                                                                                                                                                                                                                                                                 MYH9
## GO:0003824                                                                                                                                                           IGF1R/ACACA/ERBB2/AXL/CASP3/PARP1/XIAP/PRDX1/PDK1/PIK3CA/PRKCA/MAPK3/TGM2/CCND1/CDKN1A/RAF1/TYMS/SETD2/AKT1/MAPK9/CHEK1/EEF2K/PIK3R1/MSH6/PRKAA1/CASP9/ATM
## GO:0005198                                                                                                                                                                                                                                                                                                    CLDN7/CTNNA1/RPS6
## GO:0005215                                                                                                                                                                                                                                                                                                      IGF1R/BCL2/BAK1
## GO:0005488 ERBB3/FOXO3/IGF1R/ACACA/BCL2/ERBB2/AXL/BAK1/MYC/CASP3/BCL2L11/TP53/YAP1/YWHAZ/STAT3/PARP1/XIAP/CTNNB1/PRDX1/PDK1/PIK3CA/PRKCA/MAPK3/TFRC/TGM2/CCND1/EIF4G1/MYH9/CDKN1A/IRS1/JUN/RAF1/TYMS/ANXA7/CLDN7/CTNNA1/YBX1/RPS6/SRSF1/NDRG1/PECAM1/YWHAB/SETD2/AKT1/MAPK9/CHEK1/EEF2K/PIK3R1/MSH6/PRKAA1/FOXM1/CASP9/ATM/ETS1
## GO:0009055                                                                                                                                                                                                                                                                                                                     
##                    ID           Description Count GeneRatio
## GO:0000003 GO:0000003          reproduction    16     16/55
## GO:0002376 GO:0002376 immune system process    33     33/55
## GO:0008152 GO:0008152     metabolic process    50     50/55
## GO:0009987 GO:0009987      cellular process    55     55/55
## GO:0016032 GO:0016032         viral process     6      6/55
## GO:0022414 GO:0022414  reproductive process    15     15/55
##                                                                                                                                                                                                                                                                                                                               geneID
## GO:0000003                                                                                                                                                                                                                               FOXO3/IGF1R/BCL2/AXL/BAK1/CASP3/BCL2L11/STAT3/PARP1/CTNNB1/PIK3CA/MYH9/CTNNA1/AKT1/MSH6/ATM
## GO:0002376                                                                                                                               FOXO3/IGF1R/BCL2/ERBB2/AXL/BAK1/MYC/CASP3/BCL2L11/TP53/YWHAZ/STAT3/PARP1/XIAP/CTNNB1/PRDX1/PIK3CA/PRKCA/MAPK3/TFRC/MYH9/CDKN1A/RAF1/NDRG1/PECAM1/SETD2/AKT1/MAPK9/PIK3R1/MSH6/CHGA/ATM/ETS1
## GO:0008152                                 ERBB3/FOXO3/IGF1R/ACACA/BCL2/ERBB2/AXL/BAK1/MYC/CASP3/TP53/YAP1/YWHAZ/STAT3/PARP1/XIAP/CTNNB1/PRDX1/PDK1/PIK3CA/PRKCA/MAPK3/TFRC/TGM2/CCND1/EIF4G1/MYH9/CDKN1A/IRS1/JUN/RAF1/TYMS/ANXA7/YBX1/RPS6/SRSF1/PECAM1/YWHAB/SETD2/AKT1/MAPK9/CHEK1/EEF2K/PIK3R1/MSH6/PRKAA1/FOXM1/CASP9/ATM/ETS1
## GO:0009987 ERBB3/FOXO3/IGF1R/ACACA/BCL2/ERBB2/AXL/BAK1/MYC/CASP3/BCL2L11/TP53/YAP1/YWHAZ/STAT3/PARP1/XIAP/CTNNB1/PRDX1/PDK1/PIK3CA/PRKCA/MAPK3/TFRC/TGM2/CCND1/EIF4G1/MYH9/CDKN1A/IRS1/JUN/RAF1/TYMS/ANXA7/CLDN7/CTNNA1/YBX1/RPS6/SRSF1/NDRG1/PECAM1/YWHAB/SETD2/AKT1/MAPK9/CHEK1/EEF2K/PIK3R1/MSH6/PRKAA1/FOXM1/CASP9/CHGA/ATM/ETS1
## GO:0016032                                                                                                                                                                                                                                                                                               BCL2/AXL/TP53/TFRC/JUN/AKT1
## GO:0022414                                                                                                                                                                                                                                     FOXO3/IGF1R/BCL2/AXL/BAK1/CASP3/BCL2L11/PARP1/CTNNB1/PIK3CA/MYH9/CTNNA1/AKT1/MSH6/ATM
##                    ID                Description Count GeneRatio
## GO:0032991 GO:0032991 protein-containing complex    40     40/55
## GO:0044423 GO:0044423           virion component     0      0/55
## GO:0110165 GO:0110165 cellular anatomical entity    55     55/55
##                                                                                                                                                                                                                                                                                                                               geneID
## GO:0032991                                                                                       ERBB3/FOXO3/IGF1R/BCL2/ERBB2/AXL/BAK1/MYC/CASP3/BCL2L11/TP53/YAP1/STAT3/PARP1/CTNNB1/PDK1/PIK3CA/PRKCA/TFRC/TGM2/CCND1/EIF4G1/MYH9/CDKN1A/IRS1/JUN/CTNNA1/YBX1/RPS6/SRSF1/PECAM1/AKT1/CHEK1/PIK3R1/MSH6/PRKAA1/FOXM1/CASP9/ATM/ETS1
## GO:0044423                                                                                                                                                                                                                                                                                                                          
## GO:0110165 ERBB3/FOXO3/IGF1R/ACACA/BCL2/ERBB2/AXL/BAK1/MYC/CASP3/BCL2L11/TP53/YAP1/YWHAZ/STAT3/PARP1/XIAP/CTNNB1/PRDX1/PDK1/PIK3CA/PRKCA/MAPK3/TFRC/TGM2/CCND1/EIF4G1/MYH9/CDKN1A/IRS1/JUN/RAF1/TYMS/ANXA7/CLDN7/CTNNA1/YBX1/RPS6/SRSF1/NDRG1/PECAM1/YWHAB/SETD2/AKT1/MAPK9/CHEK1/EEF2K/PIK3R1/MSH6/PRKAA1/FOXM1/CASP9/CHGA/ATM/ETS1
##                    ID                  Description Count GeneRatio
## GO:0003774 GO:0003774  cytoskeletal motor activity     0       0/4
## GO:0003824 GO:0003824           catalytic activity     2       2/4
## GO:0005198 GO:0005198 structural molecule activity     0       0/4
## GO:0005215 GO:0005215         transporter activity     0       0/4
## GO:0005488 GO:0005488                      binding     4       4/4
## GO:0009055 GO:0009055   electron transfer activity     0       0/4
##                            geneID
## GO:0003774                       
## GO:0003824             AKT1/MAPK3
## GO:0005198                       
## GO:0005215                       
## GO:0005488 AKT1/MAPK3/FOXM1/YWHAB
## GO:0009055                       
##                    ID           Description Count GeneRatio
## GO:0000003 GO:0000003          reproduction     1       1/4
## GO:0002376 GO:0002376 immune system process     2       2/4
## GO:0008152 GO:0008152     metabolic process     4       4/4
## GO:0009987 GO:0009987      cellular process     4       4/4
## GO:0016032 GO:0016032         viral process     1       1/4
## GO:0022414 GO:0022414  reproductive process     1       1/4
##                            geneID
## GO:0000003                   AKT1
## GO:0002376             AKT1/MAPK3
## GO:0008152 AKT1/MAPK3/FOXM1/YWHAB
## GO:0009987 AKT1/MAPK3/FOXM1/YWHAB
## GO:0016032                   AKT1
## GO:0022414                   AKT1
##                    ID                Description Count GeneRatio
## GO:0032991 GO:0032991 protein-containing complex     2       2/4
## GO:0044423 GO:0044423           virion component     0       0/4
## GO:0110165 GO:0110165 cellular anatomical entity     4       4/4
##                            geneID
## GO:0032991             AKT1/FOXM1
## GO:0044423                       
## GO:0110165 AKT1/MAPK3/FOXM1/YWHAB
##                    ID                  Description Count GeneRatio
## GO:0003774 GO:0003774  cytoskeletal motor activity     1      1/66
## GO:0003824 GO:0003824           catalytic activity    31     31/66
## GO:0005198 GO:0005198 structural molecule activity     3      3/66
## GO:0005215 GO:0005215         transporter activity     3      3/66
## GO:0005488 GO:0005488                      binding    64     64/66
## GO:0009055 GO:0009055   electron transfer activity     0      0/66
##                                                                                                                                                                                                                                                                                                                                                                                    geneID
## GO:0003774                                                                                                                                                                                                                                                                                                                                                                           MYH9
## GO:0003824                                                                                                                                                                                              IGF1R/ACACA/ERBB2/AXL/CASP3/PARP1/XIAP/PRDX1/PDK1/PIK3CA/PRKCA/MAPK3/TGM2/CCND1/CDKN1A/RAF1/TYMS/SETD2/AKT1/MAPK9/ACVRL1/CHEK1/EEF2K/PIK3R1/MSH6/PRKAA1/CASP9/ASNS/ATM/BIRC2/PCNA
## GO:0005198                                                                                                                                                                                                                                                                                                                                                              CLDN7/CTNNA1/RPS6
## GO:0005215                                                                                                                                                                                                                                                                                                                                                                IGF1R/BCL2/BAK1
## GO:0005488 ERBB3/FOXO3/IGF1R/ACACA/BCL2/ERBB2/AXL/BAK1/MYC/CASP3/BCL2L11/TP53/YAP1/YWHAZ/STAT3/PARP1/XIAP/CTNNB1/PRDX1/PDK1/PIK3CA/PRKCA/MAPK3/TFRC/TGM2/MYH9/CCND1/CDKN1A/IRS1/JUN/RAF1/TYMS/ANXA7/CLDN7/CTNNA1/EIF4G1/YBX1/RPS6/SRSF1/NDRG1/PECAM1/YWHAB/SETD2/AKT1/PEA15/MAPK9/ACVRL1/TSC2/CHEK1/EEF2K/PIK3R1/MSH6/PRKAA1/FOXM1/CASP9/ASNS/ATM/BIRC2/PCNA/ETS1/NOTCH3/PGR/ANXA1/SQSTM1
## GO:0009055                                                                                                                                                                                                                                                                                                                                                                               
##                    ID           Description Count GeneRatio
## GO:0000003 GO:0000003          reproduction    18     18/66
## GO:0002376 GO:0002376 immune system process    36     36/66
## GO:0008152 GO:0008152     metabolic process    59     59/66
## GO:0009987 GO:0009987      cellular process    65     65/66
## GO:0016032 GO:0016032         viral process     6      6/66
## GO:0022414 GO:0022414  reproductive process    17     17/66
##                                                                                                                                                                                                                                                                                                                                                                                         geneID
## GO:0000003                                                                                                                                                                                                                                                                                FOXO3/IGF1R/BCL2/AXL/BAK1/CASP3/BCL2L11/STAT3/PARP1/CTNNB1/PIK3CA/MYH9/CTNNA1/AKT1/MSH6/ATM/PCNA/PGR
## GO:0002376                                                                                                                                                                      FOXO3/IGF1R/BCL2/ERBB2/AXL/BAK1/MYC/CASP3/BCL2L11/TP53/YWHAZ/STAT3/PARP1/XIAP/CTNNB1/PRDX1/PIK3CA/PRKCA/MAPK3/TFRC/MYH9/CDKN1A/RAF1/NDRG1/PECAM1/SETD2/AKT1/MAPK9/PIK3R1/MSH6/CHGA/ATM/BIRC2/ETS1/ANXA1/SQSTM1
## GO:0008152                                       ERBB3/FOXO3/IGF1R/ACACA/BCL2/ERBB2/AXL/BAK1/MYC/CASP3/TP53/YAP1/YWHAZ/STAT3/PARP1/XIAP/CTNNB1/PRDX1/PDK1/PIK3CA/PRKCA/MAPK3/TFRC/TGM2/MYH9/CCND1/CDKN1A/IRS1/JUN/RAF1/TYMS/ANXA7/EIF4G1/YBX1/RPS6/SRSF1/PECAM1/YWHAB/SETD2/AKT1/MAPK9/ACVRL1/TSC2/CHEK1/EEF2K/PIK3R1/MSH6/PRKAA1/FOXM1/CASP9/ASNS/ATM/BIRC2/PCNA/ETS1/NOTCH3/PGR/ANXA1/SQSTM1
## GO:0009987 ERBB3/FOXO3/IGF1R/ACACA/BCL2/ERBB2/AXL/BAK1/MYC/CASP3/BCL2L11/TP53/YAP1/YWHAZ/STAT3/PARP1/XIAP/CTNNB1/PRDX1/PDK1/PIK3CA/PRKCA/MAPK3/TFRC/TGM2/MYH9/CCND1/CDKN1A/IRS1/JUN/RAF1/TYMS/ANXA7/CLDN7/CTNNA1/EIF4G1/YBX1/RPS6/SRSF1/NDRG1/PECAM1/YWHAB/SETD2/AKT1/PEA15/MAPK9/ACVRL1/TSC2/CHEK1/EEF2K/PIK3R1/MSH6/PRKAA1/FOXM1/CASP9/CHGA/ASNS/ATM/BIRC2/PCNA/ETS1/NOTCH3/PGR/ANXA1/SQSTM1
## GO:0016032                                                                                                                                                                                                                                                                                                                                                         BCL2/AXL/TP53/TFRC/JUN/AKT1
## GO:0022414                                                                                                                                                                                                                                                                                      FOXO3/IGF1R/BCL2/AXL/BAK1/CASP3/BCL2L11/PARP1/CTNNB1/PIK3CA/MYH9/CTNNA1/AKT1/MSH6/ATM/PCNA/PGR
##                    ID                Description Count GeneRatio
## GO:0032991 GO:0032991 protein-containing complex    47     47/66
## GO:0044423 GO:0044423           virion component     0      0/66
## GO:0110165 GO:0110165 cellular anatomical entity    65     65/66
##                                                                                                                                                                                                                                                                                                                                                                                         geneID
## GO:0032991                                                                                                         ERBB3/FOXO3/IGF1R/BCL2/ERBB2/AXL/BAK1/MYC/CASP3/BCL2L11/TP53/YAP1/STAT3/PARP1/CTNNB1/PDK1/PIK3CA/PRKCA/TFRC/TGM2/MYH9/CCND1/CDKN1A/IRS1/JUN/CTNNA1/EIF4G1/YBX1/RPS6/SRSF1/PECAM1/AKT1/PEA15/ACVRL1/TSC2/CHEK1/PIK3R1/MSH6/PRKAA1/FOXM1/CASP9/ATM/BIRC2/PCNA/ETS1/NOTCH3/PGR
## GO:0044423                                                                                                                                                                                                                                                                                                                                                                                    
## GO:0110165 ERBB3/FOXO3/IGF1R/ACACA/BCL2/ERBB2/AXL/BAK1/MYC/CASP3/BCL2L11/TP53/YAP1/YWHAZ/STAT3/PARP1/XIAP/CTNNB1/PRDX1/PDK1/PIK3CA/PRKCA/MAPK3/TFRC/TGM2/MYH9/CCND1/CDKN1A/IRS1/JUN/RAF1/TYMS/ANXA7/CLDN7/CTNNA1/EIF4G1/YBX1/RPS6/SRSF1/NDRG1/PECAM1/YWHAB/SETD2/AKT1/PEA15/MAPK9/ACVRL1/TSC2/CHEK1/EEF2K/PIK3R1/MSH6/PRKAA1/FOXM1/CASP9/CHGA/ASNS/ATM/BIRC2/PCNA/ETS1/NOTCH3/PGR/ANXA1/SQSTM1
##                    ID                  Description Count GeneRatio
## GO:0003774 GO:0003774  cytoskeletal motor activity     1      1/70
## GO:0003824 GO:0003824           catalytic activity    31     31/70
## GO:0005198 GO:0005198 structural molecule activity     3      3/70
## GO:0005215 GO:0005215         transporter activity     4      4/70
## GO:0005488 GO:0005488                      binding    68     68/70
## GO:0009055 GO:0009055   electron transfer activity     0      0/70
##                                                                                                                                                                                                                                                                                                                                                                                                      geneID
## GO:0003774                                                                                                                                                                                                                                                                                                                                                                                             MYH9
## GO:0003824                                                                                                                                                                                                                IGF1R/ACACA/ERBB2/AXL/CASP3/PARP1/XIAP/PRDX1/PDK1/PIK3CA/PRKCA/MAPK3/TGM2/CCND1/CDKN1A/RAF1/TYMS/SETD2/AKT1/MAPK9/ACVRL1/CHEK1/EEF2K/PIK3R1/MSH6/PRKAA1/CASP9/ASNS/ATM/BIRC2/PCNA
## GO:0005198                                                                                                                                                                                                                                                                                                                                                                                CLDN7/CTNNA1/RPS6
## GO:0005215                                                                                                                                                                                                                                                                                                                                                                              IGF1R/BCL2/BAK1/BAX
## GO:0005488 RB1/ERBB3/FOXO3/IGF1R/ACACA/BCL2/ERBB2/AXL/BAK1/MYC/CASP3/BCL2L11/TP53/YAP1/YWHAZ/STAT3/PARP1/XIAP/CTNNB1/PRDX1/PDK1/PIK3CA/PRKCA/MAPK3/TFRC/TGM2/MYH9/CCND1/CDKN1A/IRS1/JUN/RAF1/TYMS/ANXA7/CLDN7/CTNNA1/EIF4G1/YBX1/RPS6/SRSF1/NDRG1/PECAM1/YWHAB/SETD2/AKT1/PEA15/MAPK9/ACVRL1/TSC2/CHEK1/EEF2K/PIK3R1/BCL2L1/MSH6/PRKAA1/FOXM1/BAX/CASP9/ASNS/AR/ATM/BIRC2/PCNA/ETS1/NOTCH3/PGR/ANXA1/SQSTM1
## GO:0009055                                                                                                                                                                                                                                                                                                                                                                                                 
##                    ID           Description Count GeneRatio
## GO:0000003 GO:0000003          reproduction    22     22/70
## GO:0002376 GO:0002376 immune system process    38     38/70
## GO:0008152 GO:0008152     metabolic process    62     62/70
## GO:0009987 GO:0009987      cellular process    69     69/70
## GO:0016032 GO:0016032         viral process     6      6/70
## GO:0022414 GO:0022414  reproductive process    21     21/70
##                                                                                                                                                                                                                                                                                                                                                                                                           geneID
## GO:0000003                                                                                                                                                                                                                                                                                RB1/FOXO3/IGF1R/BCL2/AXL/BAK1/CASP3/BCL2L11/STAT3/PARP1/CTNNB1/PIK3CA/MYH9/CTNNA1/AKT1/BCL2L1/MSH6/BAX/AR/ATM/PCNA/PGR
## GO:0002376                                                                                                                                                                                RB1/FOXO3/IGF1R/BCL2/ERBB2/AXL/BAK1/MYC/CASP3/BCL2L11/TP53/YWHAZ/STAT3/PARP1/XIAP/CTNNB1/PRDX1/PIK3CA/PRKCA/MAPK3/TFRC/MYH9/CDKN1A/RAF1/NDRG1/PECAM1/SETD2/AKT1/MAPK9/PIK3R1/MSH6/BAX/CHGA/ATM/BIRC2/ETS1/ANXA1/SQSTM1
## GO:0008152                                              RB1/ERBB3/FOXO3/IGF1R/ACACA/BCL2/ERBB2/AXL/BAK1/MYC/CASP3/TP53/YAP1/YWHAZ/STAT3/PARP1/XIAP/CTNNB1/PRDX1/PDK1/PIK3CA/PRKCA/MAPK3/TFRC/TGM2/MYH9/CCND1/CDKN1A/IRS1/JUN/RAF1/TYMS/ANXA7/EIF4G1/YBX1/RPS6/SRSF1/PECAM1/YWHAB/SETD2/AKT1/MAPK9/ACVRL1/TSC2/CHEK1/EEF2K/PIK3R1/MSH6/PRKAA1/FOXM1/BAX/CASP9/ASNS/AR/ATM/BIRC2/PCNA/ETS1/NOTCH3/PGR/ANXA1/SQSTM1
## GO:0009987 RB1/ERBB3/FOXO3/IGF1R/ACACA/BCL2/ERBB2/AXL/BAK1/MYC/CASP3/BCL2L11/TP53/YAP1/YWHAZ/STAT3/PARP1/XIAP/CTNNB1/PRDX1/PDK1/PIK3CA/PRKCA/MAPK3/TFRC/TGM2/MYH9/CCND1/CDKN1A/IRS1/JUN/RAF1/TYMS/ANXA7/CLDN7/CTNNA1/EIF4G1/YBX1/RPS6/SRSF1/NDRG1/PECAM1/YWHAB/SETD2/AKT1/PEA15/MAPK9/ACVRL1/TSC2/CHEK1/EEF2K/PIK3R1/BCL2L1/MSH6/PRKAA1/FOXM1/BAX/CASP9/CHGA/ASNS/AR/ATM/BIRC2/PCNA/ETS1/NOTCH3/PGR/ANXA1/SQSTM1
## GO:0016032                                                                                                                                                                                                                                                                                                                                                                           BCL2/AXL/TP53/TFRC/JUN/AKT1
## GO:0022414                                                                                                                                                                                                                                                                                      RB1/FOXO3/IGF1R/BCL2/AXL/BAK1/CASP3/BCL2L11/PARP1/CTNNB1/PIK3CA/MYH9/CTNNA1/AKT1/BCL2L1/MSH6/BAX/AR/ATM/PCNA/PGR
##                    ID                Description Count GeneRatio
## GO:0032991 GO:0032991 protein-containing complex    51     51/70
## GO:0044423 GO:0044423           virion component     0      0/70
## GO:0110165 GO:0110165 cellular anatomical entity    69     69/70
##                                                                                                                                                                                                                                                                                                                                                                                                           geneID
## GO:0032991                                                                                                         RB1/ERBB3/FOXO3/IGF1R/BCL2/ERBB2/AXL/BAK1/MYC/CASP3/BCL2L11/TP53/YAP1/STAT3/PARP1/CTNNB1/PDK1/PIK3CA/PRKCA/TFRC/TGM2/MYH9/CCND1/CDKN1A/IRS1/JUN/CTNNA1/EIF4G1/YBX1/RPS6/SRSF1/PECAM1/AKT1/PEA15/ACVRL1/TSC2/CHEK1/PIK3R1/BCL2L1/MSH6/PRKAA1/FOXM1/BAX/CASP9/AR/ATM/BIRC2/PCNA/ETS1/NOTCH3/PGR
## GO:0044423                                                                                                                                                                                                                                                                                                                                                                                                      
## GO:0110165 RB1/ERBB3/FOXO3/IGF1R/ACACA/BCL2/ERBB2/AXL/BAK1/MYC/CASP3/BCL2L11/TP53/YAP1/YWHAZ/STAT3/PARP1/XIAP/CTNNB1/PRDX1/PDK1/PIK3CA/PRKCA/MAPK3/TFRC/TGM2/MYH9/CCND1/CDKN1A/IRS1/JUN/RAF1/TYMS/ANXA7/CLDN7/CTNNA1/EIF4G1/YBX1/RPS6/SRSF1/NDRG1/PECAM1/YWHAB/SETD2/AKT1/PEA15/MAPK9/ACVRL1/TSC2/CHEK1/EEF2K/PIK3R1/BCL2L1/MSH6/PRKAA1/FOXM1/BAX/CASP9/CHGA/ASNS/AR/ATM/BIRC2/PCNA/ETS1/NOTCH3/PGR/ANXA1/SQSTM1
barplot(ggo_MF[[1]], title = "groupGO, Molecular Function, \n 3-Fold CV, alpha = 0.5, MSE")

barplot(ggo_MF[[2]], title = "groupGO, Molecular Function, \n 3-Fold CV, alpha = 0.5, AUC")

barplot(ggo_MF[[3]], title = "groupGO, Molecular Function, \n 3-Fold CV, alpha = 1, MSE")

barplot(ggo_MF[[4]], title = "groupGO, Molecular Function, \n 5-Fold CV, alpha = 0.2, MSE")

barplot(ggo_MF[[5]], title = "groupGO, Molecular Function, \n 5-Fold CV, alpha = 1, MSE")

barplot(ggo_MF[[6]], title = "groupGO, Molecular Function, \n 10-Fold CV, alpha = 0.2, MSE")

barplot(ggo_MF[[7]], title = "groupGO, Molecular Function, \n 10-Fold CV, alpha = 0.5, Deviance")

barplot(ggo_BP[[1]], title = "groupGO, Biological Process, \n 3-Fold CV, alpha = 0.5, MSE")

barplot(ggo_BP[[2]], title = "groupGO, Biological Process, \n 3-Fold CV, alpha = 0.5, AUC")

barplot(ggo_BP[[3]], title = "groupGO, Biological Process, \n 3-Fold CV, alpha = 1, MSE")

barplot(ggo_BP[[4]], title = "groupGO, Biological Process, \n 5-Fold CV, alpha = 0.2, MSE")

barplot(ggo_BP[[5]], title = "groupGO, Biological Process, \n 5-Fold CV, alpha = 1, MSE")

barplot(ggo_BP[[6]], title = "groupGO, Biological Process, \n 10-Fold CV, alpha = 0.2, MSE")

barplot(ggo_BP[[7]], title = "groupGO, Biological Process, \n 10-Fold CV, alpha = 0.5, Deviance")

barplot(ggo_CC[[1]], title = "groupGO, Cellular Component, \n 3-Fold CV, alpha = 0.5, MSE")

barplot(ggo_CC[[2]], title = "groupGO, Cellular Component, \n 3-Fold CV, alpha = 0.5, AUC")

barplot(ggo_CC[[3]], title = "groupGO, Cellular Component, \n 3-Fold CV, alpha = 1, MSE")

barplot(ggo_CC[[4]], title = "groupGO, Cellular Component, \n 5-Fold CV, alpha = 0.2, MSE")

barplot(ggo_CC[[5]], title = "groupGO, Cellular Component, \n 5-Fold CV, alpha = 1, MSE")

barplot(ggo_CC[[6]], title = "groupGO, Cellular Component, \n 10-Fold CV, alpha = 0.2, MSE")

barplot(ggo_CC[[7]], title = "groupGO, Cellular Component, \n 10-Fold CV, alpha = 0.5, Deviance")

B. GO Over-Representation

ego_MF <- list()#GO enrichment of a geneset for Molecular Function
ego_BP <- list()#GO enrichment of a geneset for Biological Process
ego_CC <- list()#GO enrichment of a geneset for Cellular Component


for(z in 1:length(geneNames)){
  print(z)
  input <- geneNames[[z]]
  ego_MF[[z]] <- enrichGO(
    gene          = input,
    OrgDb         = org.Hs.eg.db,
    ont           = "MF",
    pAdjustMethod = "BH",
    keyType="SYMBOL",
    pvalueCutoff  = 0.05,
    qvalueCutoff  = 0.05,
    minGSSize     = 2,
    readable      = TRUE)
  
  ego_BP[[z]] <- enrichGO(
    gene          = input,
    OrgDb         = org.Hs.eg.db,
    ont           = "BP",
    pAdjustMethod = "BH",
    keyType="SYMBOL",
    pvalueCutoff  = 0.05,
    qvalueCutoff  = 0.05,
    minGSSize     = 2,
    readable      = TRUE)
  
  ego_CC[[z]] <- enrichGO(
    gene          = input,
    OrgDb         = org.Hs.eg.db,
    ont           = "CC",
    pAdjustMethod = "BH",
    keyType="SYMBOL",
    pvalueCutoff  = 0.05,
    qvalueCutoff  = 0.05,
    minGSSize     = 2,
    readable      = TRUE)
}
## [1] 1
## [1] 2
## [1] 3
## [1] 4
## [1] 5
## [1] 6
## [1] 7
for(z in 1:length(geneNames)){
  print(head(ego_MF[[z]]))
  print(head(ego_BP[[z]]))
  print(head(ego_CC[[z]]))
}
##                    ID                              Description GeneRatio
## GO:0004674 GO:0004674 protein serine/threonine kinase activity     14/71
## GO:0043125 GO:0043125            ErbB-3 class receptor binding      4/71
## GO:0106310 GO:0106310           protein serine kinase activity     12/71
## GO:0140297 GO:0140297 DNA-binding transcription factor binding     13/71
## GO:0031625 GO:0031625         ubiquitin protein ligase binding     10/71
## GO:0001221 GO:0001221        transcription coregulator binding      7/71
##              BgRatio       pvalue     p.adjust       qvalue
## GO:0004674 427/18522 7.049681e-10 1.783577e-07 8.009065e-08
## GO:0043125   5/18522 9.881314e-10 1.783577e-07 8.009065e-08
## GO:0106310 363/18522 1.213357e-08 1.460074e-06 6.556388e-07
## GO:0140297 478/18522 2.844093e-08 2.566794e-06 1.152606e-06
## GO:0031625 305/18522 2.405162e-07 1.606434e-05 7.213614e-06
## GO:0001221 114/18522 2.669974e-07 1.606434e-05 7.213614e-06
##                                                                                     geneID
## GO:0004674 AKT1/CHEK1/CDK1/RAF1/AKT3/GSK3B/MAPK1/STK11/MAPK3/ACVRL1/EEF2K/PRKAA1/ATM/MAPK9
## GO:0043125                                                         ERBB2/PIK3R1/ERBB3/NRG1
## GO:0106310              AKT1/CHEK1/CDK1/RAF1/AKT3/GSK3B/MAPK1/STK11/MAPK3/PRKAA1/ATM/MAPK9
## GO:0140297                AR/RB1/E2F1/MYC/GSK3B/MAPK3/JUN/TP53/CTNNB1/YAP1/PCNA/SMAD4/ETS1
## GO:0031625                      RB1/TUBA1B/BECN1/ERBB3/GSK3B/CDKN1A/JUN/TP53/CTNNB1/SQSTM1
## GO:0001221                                              AR/FOXO3/MYC/CTNNB1/SMAD4/ETS1/PGR
##            Count
## GO:0004674    14
## GO:0043125     4
## GO:0106310    12
## GO:0140297    13
## GO:0031625    10
## GO:0001221     7
##                    ID                                 Description GeneRatio
## GO:0048732 GO:0048732                           gland development     21/72
## GO:0050673 GO:0050673               epithelial cell proliferation     21/72
## GO:0097193 GO:0097193       intrinsic apoptotic signaling pathway     18/72
## GO:0071214 GO:0071214       cellular response to abiotic stimulus     17/72
## GO:0104004 GO:0104004 cellular response to environmental stimulus     17/72
## GO:0070482 GO:0070482                   response to oxygen levels     17/72
##              BgRatio       pvalue     p.adjust       qvalue
## GO:0048732 449/18888 1.255727e-17 4.568333e-14 1.896808e-14
## GO:0050673 482/18888 5.275417e-17 9.595983e-14 3.984328e-14
## GO:0097193 319/18888 1.407215e-16 1.706482e-13 7.085449e-14
## GO:0071214 334/18888 6.054784e-15 4.405461e-12 1.829182e-12
## GO:0104004 334/18888 6.054784e-15 4.405461e-12 1.829182e-12
## GO:0070482 354/18888 1.575864e-14 9.554988e-12 3.967306e-12
##                                                                                                                        geneID
## GO:0048732 NOTCH1/CCND1/AKT1/AR/FASN/SRSF1/BCL2L11/RAF1/XBP1/ITGA2/MAPK1/STK11/MAPK3/BAX/CTNNB1/ATM/PCNA/SMAD4/NRG1/PGR/SNAI2
## GO:0050673   NOTCH1/ERBB2/CCND1/AKT1/BCL2L1/AR/RB1/MYC/RAF1/XBP1/AKT3/KDR/CDKN1A/MAPK1/STK11/ACVRL1/BAX/CTNNB1/YAP1/PGR/SNAI2
## GO:0097193              AKT1/BCL2L1/PIK3R1/BECN1/E2F1/MYC/BCL2L11/XBP1/MSH6/CDKN1A/STK11/BAX/CASP9/PDK1/TP53/CTNNB1/ATM/SNAI2
## GO:0071214                   BCL2L1/PIK3R1/CHEK1/IGF1R/MYC/ITGA2/CDKN1A/STK11/MAPK3/RAB11B/BAX/CASP9/TP53/YAP1/ATM/PCNA/SNAI2
## GO:0104004                   BCL2L1/PIK3R1/CHEK1/IGF1R/MYC/ITGA2/CDKN1A/STK11/MAPK3/RAB11B/BAX/CASP9/TP53/YAP1/ATM/PCNA/SNAI2
## GO:0070482                  NOTCH1/AKT1/BECN1/FOXO3/MYC/ITGA2/CDKN1A/ACVRL1/EEF2K/PRKAA1/CASP9/PDK1/TFRC/TP53/ATM/BIRC2/SMAD4
##            Count
## GO:0048732    21
## GO:0050673    21
## GO:0097193    18
## GO:0071214    17
## GO:0104004    17
## GO:0070482    17
##                    ID
## GO:1902911 GO:1902911
## GO:0061695 GO:0061695
## GO:0005741 GO:0005741
## GO:0000307 GO:0000307
## GO:0031968 GO:0031968
## GO:0019867 GO:0019867
##                                                               Description
## GO:1902911                                         protein kinase complex
## GO:0061695 transferase complex, transferring phosphorus-containing groups
## GO:0005741                                   mitochondrial outer membrane
## GO:0000307             cyclin-dependent protein kinase holoenzyme complex
## GO:0031968                                       organelle outer membrane
## GO:0019867                                                 outer membrane
##            GeneRatio   BgRatio       pvalue     p.adjust       qvalue
## GO:1902911      8/72 150/19894 6.892704e-08 1.847245e-05 1.052044e-05
## GO:0061695     10/72 308/19894 1.570194e-07 2.104060e-05 1.198306e-05
## GO:0005741      8/72 219/19894 1.240321e-06 1.108020e-04 6.310407e-05
## GO:0000307      5/72  56/19894 1.784398e-06 1.195546e-04 6.808886e-05
## GO:0031968      8/72 248/19894 3.133960e-06 1.473968e-04 8.394557e-05
## GO:0019867      8/72 250/19894 3.325891e-06 1.473968e-04 8.394557e-05
##                                                                geneID Count
## GO:1902911              CCND1/RB1/IGF1R/CDK1/CDKN1A/STK11/PRKAA1/PCNA     8
## GO:0061695 CCND1/RB1/PIK3R1/IGF1R/CDK1/BECN1/CDKN1A/STK11/PRKAA1/PCNA    10
## GO:0005741               KRAS/BCL2L1/BECN1/FOXO3/BCL2L11/RAF1/BAX/PGR     8
## GO:0000307                                 CCND1/RB1/CDK1/CDKN1A/PCNA     5
## GO:0031968               KRAS/BCL2L1/BECN1/FOXO3/BCL2L11/RAF1/BAX/PGR     8
## GO:0019867               KRAS/BCL2L1/BECN1/FOXO3/BCL2L11/RAF1/BAX/PGR     8
##                    ID                               Description GeneRatio
## GO:0019887 GO:0019887         protein kinase regulator activity      4/14
## GO:0019207 GO:0019207                 kinase regulator activity      4/14
## GO:0001221 GO:0001221         transcription coregulator binding      3/14
## GO:0045309 GO:0045309 protein phosphorylated amino acid binding      2/14
## GO:0004860 GO:0004860         protein kinase inhibitor activity      2/14
## GO:0003989 GO:0003989           acetyl-CoA carboxylase activity      1/14
##              BgRatio       pvalue    p.adjust       qvalue
## GO:0019887 232/18522 2.175551e-05 0.002107870 0.0007465156
## GO:0019207 270/18522 3.939943e-05 0.002107870 0.0007465156
## GO:0001221 114/18522 7.867077e-05 0.002805924 0.0009937361
## GO:0045309  59/18522 8.856817e-04 0.017119598 0.0060630154
## GO:0004860  73/18522 1.352161e-03 0.017119598 0.0060630154
## GO:0003989   2/18522 1.511185e-03 0.017119598 0.0060630154
##                            geneID Count
## GO:0019887 ERBB3/CCND1/AKT1/YWHAB     4
## GO:0019207 ERBB3/CCND1/AKT1/YWHAB     4
## GO:0001221         FOXO3/MYC/ETS1     3
## GO:0045309            MAPK3/YWHAB     2
## GO:0004860             AKT1/YWHAB     2
## GO:0003989                  ACACA     1
##                    ID                                   Description GeneRatio
## GO:0072331 GO:0072331     signal transduction by p53 class mediator      5/15
## GO:0042770 GO:0042770 signal transduction in response to DNA damage      5/15
## GO:0051347 GO:0051347   positive regulation of transferase activity      6/15
## GO:0044772 GO:0044772           mitotic cell cycle phase transition      6/15
## GO:0097306 GO:0097306                  cellular response to alcohol      4/15
## GO:0097305 GO:0097305                           response to alcohol      5/15
##              BgRatio       pvalue     p.adjust       qvalue
## GO:0072331 177/18888 1.900682e-07 0.0001165852 5.017132e-05
## GO:0042770 188/18888 2.565495e-07 0.0001165852 5.017132e-05
## GO:0051347 376/18888 2.571731e-07 0.0001165852 5.017132e-05
## GO:0044772 451/18888 7.473915e-07 0.0002460387 1.058804e-04
## GO:0097306 106/18888 1.219604e-06 0.0002460387 1.058804e-04
## GO:0097305 259/18888 1.251969e-06 0.0002460387 1.058804e-04
##                                       geneID Count
## GO:0072331        FOXO3/MYC/AKT1/CHEK1/FOXM1     5
## GO:0042770     FOXO3/CCND1/MAPK3/CHEK1/FOXM1     5
## GO:0051347  ERBB3/IGF1R/CCND1/MYC/AKT1/MAPK3     6
## GO:0044772 CCND1/MYC/EIF4G1/AKT1/CHEK1/FOXM1     6
## GO:0097306            FOXO3/IGF1R/ACACA/AKT1     4
## GO:0097305     FOXO3/IGF1R/ACACA/EIF4G1/AKT1     5
##                    ID                                       Description
## GO:0017053 GO:0017053                   transcription repressor complex
## GO:0090571 GO:0090571 RNA polymerase II transcription repressor complex
## GO:0038143 GO:0038143                               ERBB3:ERBB2 complex
## GO:0071943 GO:0071943                                   Myc-Max complex
## GO:0097128 GO:0097128                            cyclin D1-CDK4 complex
## GO:0005901 GO:0005901                                           caveola
##            GeneRatio  BgRatio       pvalue    p.adjust      qvalue
## GO:0017053      3/15 77/19894 2.453163e-05 0.001643619 0.001084556
## GO:0090571      2/15 15/19894 5.540208e-05 0.001855970 0.001224678
## GO:0038143      1/15  2/19894 1.507462e-03 0.019004610 0.012540356
## GO:0071943      1/15  2/19894 1.507462e-03 0.019004610 0.012540356
## GO:0097128      1/15  2/19894 1.507462e-03 0.019004610 0.012540356
## GO:0005901      2/15 82/19894 1.701905e-03 0.019004610 0.012540356
##                     geneID Count
## GO:0017053 FOXO3/CCND1/MYC     3
## GO:0090571       FOXO3/MYC     2
## GO:0038143           ERBB3     1
## GO:0071943             MYC     1
## GO:0097128           CCND1     1
## GO:0005901     IGF1R/MAPK3     2
##                    ID                              Description GeneRatio
## GO:0004674 GO:0004674 protein serine/threonine kinase activity      5/20
## GO:0019887 GO:0019887        protein kinase regulator activity      4/20
## GO:0004707 GO:0004707                      MAP kinase activity      2/20
## GO:0019207 GO:0019207                kinase regulator activity      4/20
## GO:0001221 GO:0001221        transcription coregulator binding      3/20
## GO:0030295 GO:0030295        protein kinase activator activity      3/20
##              BgRatio       pvalue    p.adjust      qvalue
## GO:0004674 427/18522 7.408307e-05 0.006103321 0.002264769
## GO:0019887 232/18522 9.925604e-05 0.006103321 0.002264769
## GO:0004707  16/18522 1.317264e-04 0.006103321 0.002264769
## GO:0019207 270/18522 1.779924e-04 0.006185235 0.002295165
## GO:0001221 114/18522 2.398379e-04 0.006667495 0.002474118
## GO:0030295 129/18522 3.450128e-04 0.006825483 0.002532743
##                                   geneID Count
## GO:0004674 AKT1/MAPK3/ACVRL1/EEF2K/MAPK9     5
## GO:0019887       ERBB3/CCND1/AKT1/CDKN1A     4
## GO:0004707                   MAPK3/MAPK9     2
## GO:0019207       ERBB3/CCND1/AKT1/CDKN1A     4
## GO:0001221                FOXO3/MYC/ETS1     3
## GO:0030295            ERBB3/CCND1/CDKN1A     3
##                    ID                                 Description GeneRatio
## GO:0009411 GO:0009411                              response to UV      6/21
## GO:0031667 GO:0031667                 response to nutrient levels      8/21
## GO:0070482 GO:0070482                   response to oxygen levels      7/21
## GO:1901655 GO:1901655                 cellular response to ketone      5/21
## GO:1901654 GO:1901654                          response to ketone      6/21
## GO:0051347 GO:0051347 positive regulation of transferase activity      7/21
##              BgRatio       pvalue     p.adjust       qvalue
## GO:0009411 154/18888 1.306671e-08 2.247474e-05 9.504314e-06
## GO:0031667 490/18888 2.930357e-08 2.520107e-05 1.065725e-05
## GO:0070482 354/18888 7.101610e-08 3.070923e-05 1.298658e-05
## GO:1901655 107/18888 1.005224e-07 3.070923e-05 1.298658e-05
## GO:1901654 217/18888 1.008309e-07 3.070923e-05 1.298658e-05
## GO:0051347 376/18888 1.071252e-07 3.070923e-05 1.298658e-05
##                                                   geneID Count
## GO:0009411               CCND1/MYC/AKT1/CDKN1A/BAX/CASP9     6
## GO:0031667 FOXO3/IGF1R/EIF4G1/AKT1/CDKN1A/MAPK3/BAX/ASNS     8
## GO:0070482      FOXO3/MYC/AKT1/CDKN1A/ACVRL1/EEF2K/CASP9     7
## GO:1901655                  FOXO3/IGF1R/ACACA/AKT1/CASP9     5
## GO:1901654           FOXO3/IGF1R/ACACA/AKT1/CDKN1A/CASP9     6
## GO:0051347       ERBB3/IGF1R/CCND1/MYC/AKT1/CDKN1A/MAPK3     7
##                    ID                                        Description
## GO:0017053 GO:0017053                    transcription repressor complex
## GO:0090571 GO:0090571  RNA polymerase II transcription repressor complex
## GO:1902911 GO:1902911                             protein kinase complex
## GO:0000307 GO:0000307 cyclin-dependent protein kinase holoenzyme complex
## GO:0038143 GO:0038143                                ERBB3:ERBB2 complex
## GO:0070557 GO:0070557                                   PCNA-p21 complex
##            GeneRatio   BgRatio       pvalue    p.adjust      qvalue
## GO:0017053      3/21  77/19894 7.051822e-05 0.005525745 0.002908287
## GO:0090571      2/21  15/19894 1.105149e-04 0.005525745 0.002908287
## GO:1902911      3/21 150/19894 5.057831e-04 0.016859436 0.008873387
## GO:0000307      2/21  56/19894 1.579160e-03 0.023334521 0.012281327
## GO:0038143      1/21   2/19894 2.110128e-03 0.023334521 0.012281327
## GO:0070557      1/21   2/19894 2.110128e-03 0.023334521 0.012281327
##                        geneID Count
## GO:0017053    FOXO3/CCND1/MYC     3
## GO:0090571          FOXO3/MYC     2
## GO:1902911 IGF1R/CCND1/CDKN1A     3
## GO:0000307       CCND1/CDKN1A     2
## GO:0038143              ERBB3     1
## GO:0070557             CDKN1A     1
##                    ID                               Description GeneRatio
## GO:0140297 GO:0140297  DNA-binding transcription factor binding     11/54
## GO:0043125 GO:0043125             ErbB-3 class receptor binding      3/54
## GO:0004674 GO:0004674  protein serine/threonine kinase activity     10/54
## GO:0035173 GO:0035173                   histone kinase activity      4/54
## GO:0045309 GO:0045309 protein phosphorylated amino acid binding      5/54
## GO:0043548 GO:0043548     phosphatidylinositol 3-kinase binding      4/54
##              BgRatio       pvalue     p.adjust       qvalue
## GO:0140297 478/18522 1.060015e-07 3.360246e-05 1.539811e-05
## GO:0043125   5/18522 2.332834e-07 3.697542e-05 1.694374e-05
## GO:0004674 427/18522 3.690298e-07 3.899414e-05 1.786881e-05
## GO:0035173  23/18522 5.482580e-07 4.120201e-05 1.888055e-05
## GO:0045309  59/18522 7.740765e-07 4.120201e-05 1.888055e-05
## GO:0043548  25/18522 7.798488e-07 4.120201e-05 1.888055e-05
##                                                                geneID Count
## GO:0140297 BCL2/MYC/TP53/YAP1/YWHAZ/STAT3/PARP1/CTNNB1/MAPK3/JUN/ETS1    11
## GO:0043125                                         ERBB3/ERBB2/PIK3R1     3
## GO:0004674  PIK3CA/PRKCA/MAPK3/RAF1/AKT1/MAPK9/CHEK1/EEF2K/PRKAA1/ATM    10
## GO:0035173                                     PRKCA/CHEK1/PRKAA1/ATM     4
## GO:0045309                              YWHAZ/MAPK3/IRS1/YWHAB/PIK3R1     5
## GO:0043548                                      IGF1R/AXL/IRS1/PIK3R1     4
##                    ID                            Description GeneRatio
## GO:0009411 GO:0009411                         response to UV     13/55
## GO:0097193 GO:0097193  intrinsic apoptotic signaling pathway     15/55
## GO:0010332 GO:0010332            response to gamma radiation      9/55
## GO:0051402 GO:0051402               neuron apoptotic process     14/55
## GO:0043523 GO:0043523 regulation of neuron apoptotic process     13/55
## GO:0097305 GO:0097305                    response to alcohol     13/55
##              BgRatio       pvalue     p.adjust       qvalue
## GO:0009411 154/18888 4.546674e-16 1.425382e-12 6.159546e-13
## GO:0097193 319/18888 1.209443e-14 1.895801e-11 8.192382e-12
## GO:0010332  52/18888 2.529209e-14 2.643023e-11 1.142137e-11
## GO:0051402 292/18888 8.050039e-14 6.309218e-11 2.726421e-11
## GO:0043523 244/18888 1.817492e-13 1.139567e-10 4.924446e-11
## GO:0097305 259/18888 3.899605e-13 1.757690e-10 7.595558e-11
##                                                                                          geneID
## GO:0009411            BCL2/BAK1/MYC/CASP3/TP53/PARP1/CCND1/CDKN1A/AKT1/PIK3R1/MSH6/PRKAA1/CASP9
## GO:0097193 BCL2/BAK1/MYC/CASP3/BCL2L11/TP53/PARP1/CTNNB1/PDK1/CDKN1A/AKT1/PIK3R1/MSH6/CASP9/ATM
## GO:0010332                                      BCL2/BAK1/MYC/TP53/YAP1/PARP1/CDKN1A/PRKAA1/ATM
## GO:0051402     ERBB3/FOXO3/BCL2/AXL/CASP3/BCL2L11/TP53/PARP1/XIAP/CTNNB1/PIK3CA/CCND1/CASP9/ATM
## GO:0043523          ERBB3/FOXO3/BCL2/AXL/CASP3/BCL2L11/TP53/PARP1/CTNNB1/PIK3CA/CCND1/CASP9/ATM
## GO:0097305      FOXO3/IGF1R/ACACA/BAK1/PARP1/CTNNB1/EIF4G1/CDKN1A/TYMS/CLDN7/CTNNA1/AKT1/PRKAA1
##            Count
## GO:0009411    13
## GO:0097193    15
## GO:0010332     9
## GO:0051402    14
## GO:0043523    13
## GO:0097305    13
##                    ID                                       Description
## GO:0017053 GO:0017053                   transcription repressor complex
## GO:0097136 GO:0097136                      Bcl-2 family protein complex
## GO:0005901 GO:0005901                                           caveola
## GO:0038143 GO:0038143                               ERBB3:ERBB2 complex
## GO:0090571 GO:0090571 RNA polymerase II transcription repressor complex
## GO:0044853 GO:0044853                              plasma membrane raft
##            GeneRatio   BgRatio       pvalue     p.adjust       qvalue
## GO:0017053      5/55  77/19894 2.277285e-06 0.0002261493 0.0001179340
## GO:0097136      3/55  10/19894 2.366726e-06 0.0002261493 0.0001179340
## GO:0005901      5/55  82/19894 3.112146e-06 0.0002261493 0.0001179340
## GO:0038143      2/55   2/19894 7.504712e-06 0.0003874416 0.0002020458
## GO:0090571      3/55  15/19894 8.886276e-06 0.0003874416 0.0002020458
## GO:0044853      5/55 113/19894 1.500382e-05 0.0005451389 0.0002842830
##                                    geneID Count
## GO:0017053    FOXO3/MYC/TP53/CTNNB1/CCND1     5
## GO:0097136              BCL2/BAK1/BCL2L11     3
## GO:0005901 IGF1R/CTNNB1/MAPK3/IRS1/CTNNA1     5
## GO:0038143                    ERBB3/ERBB2     2
## GO:0090571               FOXO3/MYC/CTNNB1     3
## GO:0044853 IGF1R/CTNNB1/MAPK3/IRS1/CTNNA1     5
##                    ID                               Description GeneRatio
## GO:0045309 GO:0045309 protein phosphorylated amino acid binding       2/4
## GO:0004860 GO:0004860         protein kinase inhibitor activity       2/4
## GO:0019210 GO:0019210                 kinase inhibitor activity       2/4
## GO:0051219 GO:0051219                    phosphoprotein binding       2/4
## GO:0019887 GO:0019887         protein kinase regulator activity       2/4
## GO:0099104 GO:0099104      potassium channel activator activity       1/4
##              BgRatio       pvalue    p.adjust       qvalue      geneID Count
## GO:0045309  59/18522 5.960670e-05 0.001149206 0.0001466291 MAPK3/YWHAB     2
## GO:0004860  73/18522 9.146013e-05 0.001149206 0.0001466291  AKT1/YWHAB     2
## GO:0019210  78/18522 1.044732e-04 0.001149206 0.0001466291  AKT1/YWHAB     2
## GO:0051219  93/18522 1.486690e-04 0.001226519 0.0001564936 MAPK3/YWHAB     2
## GO:0019887 232/18522 9.218946e-04 0.004986238 0.0006362027  AKT1/YWHAB     2
## GO:0099104   5/18522 1.079447e-03 0.004986238 0.0006362027        AKT1     1
##                    ID
## GO:0051054 GO:0051054
## GO:0032872 GO:0032872
## GO:0071276 GO:0071276
## GO:0070302 GO:0070302
## GO:0014044 GO:0014044
## GO:0070849 GO:0070849
##                                                                Description
## GO:0051054                    positive regulation of DNA metabolic process
## GO:0032872                     regulation of stress-activated MAPK cascade
## GO:0071276                                cellular response to cadmium ion
## GO:0070302 regulation of stress-activated protein kinase signaling cascade
## GO:0014044                                        Schwann cell development
## GO:0070849                             response to epidermal growth factor
##            GeneRatio   BgRatio       pvalue    p.adjust       qvalue
## GO:0051054       3/4 301/18888 1.584016e-05 0.003498466 0.0008218221
## GO:0032872       2/4  35/18888 1.996811e-05 0.003498466 0.0008218221
## GO:0071276       2/4  37/18888 2.234770e-05 0.003498466 0.0008218221
## GO:0070302       2/4  38/18888 2.358757e-05 0.003498466 0.0008218221
## GO:0014044       2/4  42/18888 2.888073e-05 0.003498466 0.0008218221
## GO:0070849       2/4  46/18888 3.470744e-05 0.003498466 0.0008218221
##                      geneID Count
## GO:0051054 AKT1/MAPK3/FOXM1     3
## GO:0032872      MAPK3/FOXM1     2
## GO:0071276       AKT1/MAPK3     2
## GO:0070302      MAPK3/FOXM1     2
## GO:0014044       AKT1/MAPK3     2
## GO:0070849       AKT1/MAPK3     2
##                    ID             Description GeneRatio   BgRatio      pvalue
## GO:0098978 GO:0098978   glutamatergic synapse       2/4 409/19894 0.002461462
## GO:0005925 GO:0005925          focal adhesion       2/4 421/19894 0.002606078
## GO:0030055 GO:0030055 cell-substrate junction       2/4 431/19894 0.002729650
## GO:0031143 GO:0031143            pseudopodium       1/4  18/19894 0.003614545
##              p.adjust     qvalue      geneID Count
## GO:0098978 0.01807272 0.00951196  AKT1/MAPK3     2
## GO:0005925 0.01807272 0.00951196 MAPK3/YWHAB     2
## GO:0030055 0.01807272 0.00951196 MAPK3/YWHAB     2
## GO:0031143 0.01807272 0.00951196       MAPK3     1
##                    ID                              Description GeneRatio
## GO:0140297 GO:0140297 DNA-binding transcription factor binding     12/64
## GO:0004674 GO:0004674 protein serine/threonine kinase activity     11/64
## GO:0030971 GO:0030971         receptor tyrosine kinase binding      6/64
## GO:0043125 GO:0043125            ErbB-3 class receptor binding      3/64
## GO:0031625 GO:0031625         ubiquitin protein ligase binding      9/64
## GO:0035173 GO:0035173                  histone kinase activity      4/64
##              BgRatio       pvalue     p.adjust       qvalue
## GO:0140297 478/18522 7.391982e-08 2.661113e-05 1.244965e-05
## GO:0004674 427/18522 2.130897e-07 3.523815e-05 1.648568e-05
## GO:0030971  81/18522 3.549755e-07 3.523815e-05 1.648568e-05
## GO:0043125   5/18522 3.915350e-07 3.523815e-05 1.648568e-05
## GO:0031625 305/18522 9.848097e-07 6.554912e-05 3.066625e-05
## GO:0035173  23/18522 1.092485e-06 6.554912e-05 3.066625e-05
##                                                                      geneID
## GO:0140297  BCL2/MYC/TP53/YAP1/YWHAZ/STAT3/PARP1/CTNNB1/MAPK3/JUN/PCNA/ETS1
## GO:0004674 PIK3CA/PRKCA/MAPK3/RAF1/AKT1/MAPK9/ACVRL1/CHEK1/EEF2K/PRKAA1/ATM
## GO:0030971                               ERBB2/TP53/IRS1/PIK3R1/PCNA/SQSTM1
## GO:0043125                                               ERBB3/ERBB2/PIK3R1
## GO:0031625             ERBB3/BCL2/TP53/YWHAZ/PARP1/CTNNB1/CDKN1A/JUN/SQSTM1
## GO:0035173                                           PRKCA/CHEK1/PRKAA1/ATM
##            Count
## GO:0140297    12
## GO:0004674    11
## GO:0030971     6
## GO:0043125     3
## GO:0031625     9
## GO:0035173     4
##                    ID                           Description GeneRatio   BgRatio
## GO:0009411 GO:0009411                        response to UV     14/65 154/18888
## GO:0070482 GO:0070482             response to oxygen levels     16/65 354/18888
## GO:0010332 GO:0010332           response to gamma radiation      9/65  52/18888
## GO:0000302 GO:0000302   response to reactive oxygen species     13/65 203/18888
## GO:0097193 GO:0097193 intrinsic apoptotic signaling pathway     15/65 319/18888
## GO:0031960 GO:0031960            response to corticosteroid     12/65 156/18888
##                  pvalue     p.adjust       qvalue
## GO:0009411 1.341650e-16 4.424762e-13 2.008238e-13
## GO:0070482 4.659647e-14 7.683758e-11 3.487378e-11
## GO:0010332 1.245693e-13 9.012880e-11 4.090618e-11
## GO:0000302 1.744763e-13 9.012880e-11 4.090618e-11
## GO:0097193 1.810339e-13 9.012880e-11 4.090618e-11
## GO:0031960 1.814404e-13 9.012880e-11 4.090618e-11
##                                                                                               geneID
## GO:0009411            BCL2/BAK1/MYC/CASP3/TP53/PARP1/CCND1/CDKN1A/AKT1/PIK3R1/MSH6/PRKAA1/CASP9/PCNA
## GO:0070482 FOXO3/BCL2/MYC/CASP3/TP53/PDK1/TFRC/CDKN1A/NDRG1/AKT1/ACVRL1/EEF2K/PRKAA1/CASP9/ATM/BIRC2
## GO:0010332                                           BCL2/BAK1/MYC/TP53/YAP1/PARP1/CDKN1A/PRKAA1/ATM
## GO:0000302                      FOXO3/BCL2/AXL/BAK1/CASP3/PRDX1/MAPK3/JUN/AKT1/MAPK9/PRKAA1/ATM/PCNA
## GO:0097193      BCL2/BAK1/MYC/CASP3/BCL2L11/TP53/PARP1/CTNNB1/PDK1/CDKN1A/AKT1/PIK3R1/MSH6/CASP9/ATM
## GO:0031960                  FOXO3/IGF1R/BCL2/CASP3/BCL2L11/PARP1/PIK3CA/CDKN1A/TYMS/CASP9/PCNA/ANXA1
##            Count
## GO:0009411    14
## GO:0070482    16
## GO:0010332     9
## GO:0000302    13
## GO:0097193    15
## GO:0031960    12
##                    ID
## GO:0097136 GO:0097136
## GO:0017053 GO:0017053
## GO:0061695 GO:0061695
## GO:0005901 GO:0005901
## GO:1902911 GO:1902911
## GO:0038143 GO:0038143
##                                                               Description
## GO:0097136                                   Bcl-2 family protein complex
## GO:0017053                                transcription repressor complex
## GO:0061695 transferase complex, transferring phosphorus-containing groups
## GO:0005901                                                        caveola
## GO:1902911                                         protein kinase complex
## GO:0038143                                            ERBB3:ERBB2 complex
##            GeneRatio   BgRatio       pvalue     p.adjust       qvalue
## GO:0097136      3/65  10/19894 3.930082e-06 0.0003694095 0.0002054909
## GO:0017053      5/65  77/19894 5.246600e-06 0.0003694095 0.0002054909
## GO:0061695      8/65 308/19894 7.072064e-06 0.0003694095 0.0002054909
## GO:0005901      5/65  82/19894 7.155088e-06 0.0003694095 0.0002054909
## GO:1902911      6/65 150/19894 9.515754e-06 0.0003694095 0.0002054909
## GO:0038143      2/65   2/19894 1.051165e-05 0.0003694095 0.0002054909
##                                                       geneID Count
## GO:0097136                                 BCL2/BAK1/BCL2L11     3
## GO:0017053                       FOXO3/MYC/TP53/CTNNB1/CCND1     5
## GO:0061695 IGF1R/PIK3CA/CCND1/CDKN1A/IRS1/PIK3R1/PRKAA1/PCNA     8
## GO:0005901                    IGF1R/CTNNB1/MAPK3/IRS1/CTNNA1     5
## GO:1902911               IGF1R/CCND1/CDKN1A/IRS1/PRKAA1/PCNA     6
## GO:0038143                                       ERBB3/ERBB2     2
##                    ID                              Description GeneRatio
## GO:0140297 GO:0140297 DNA-binding transcription factor binding     14/68
## GO:0051400 GO:0051400                        BH domain binding      4/68
## GO:0031625 GO:0031625         ubiquitin protein ligase binding     10/68
## GO:0044389 GO:0044389    ubiquitin-like protein ligase binding     10/68
## GO:0004674 GO:0004674 protein serine/threonine kinase activity     11/68
## GO:0043125 GO:0043125            ErbB-3 class receptor binding      3/68
##              BgRatio       pvalue     p.adjust       qvalue
## GO:0140297 478/18522 1.657329e-09 6.016105e-07 2.704063e-07
## GO:0051400   9/18522 2.064379e-08 3.746848e-06 1.684099e-06
## GO:0031625 305/18522 1.581950e-07 1.914159e-05 8.603587e-06
## GO:0044389 324/18522 2.765490e-07 2.509682e-05 1.128029e-05
## GO:0004674 427/18522 4.044292e-07 2.650277e-05 1.191222e-05
## GO:0043125   5/18522 4.708093e-07 2.650277e-05 1.191222e-05
##                                                                            geneID
## GO:0140297 RB1/BCL2/MYC/TP53/YAP1/YWHAZ/STAT3/PARP1/CTNNB1/MAPK3/JUN/AR/PCNA/ETS1
## GO:0051400                                                   BCL2/BAK1/BCL2L1/BAX
## GO:0031625               RB1/ERBB3/BCL2/TP53/YWHAZ/PARP1/CTNNB1/CDKN1A/JUN/SQSTM1
## GO:0044389               RB1/ERBB3/BCL2/TP53/YWHAZ/PARP1/CTNNB1/CDKN1A/JUN/SQSTM1
## GO:0004674       PIK3CA/PRKCA/MAPK3/RAF1/AKT1/MAPK9/ACVRL1/CHEK1/EEF2K/PRKAA1/ATM
## GO:0043125                                                     ERBB3/ERBB2/PIK3R1
##            Count
## GO:0140297    14
## GO:0051400     4
## GO:0031625    10
## GO:0044389    10
## GO:0004674    11
## GO:0043125     3
##                    ID                                 Description GeneRatio
## GO:0009411 GO:0009411                              response to UV     15/69
## GO:0010332 GO:0010332                 response to gamma radiation     11/69
## GO:0051402 GO:0051402                    neuron apoptotic process     17/69
## GO:0097193 GO:0097193       intrinsic apoptotic signaling pathway     17/69
## GO:0071214 GO:0071214       cellular response to abiotic stimulus     17/69
## GO:0104004 GO:0104004 cellular response to environmental stimulus     17/69
##              BgRatio       pvalue     p.adjust       qvalue
## GO:0009411 154/18888 9.067192e-18 3.095539e-14 1.346717e-14
## GO:0010332  52/18888 3.598885e-17 6.143296e-14 2.672645e-14
## GO:0051402 292/18888 2.991223e-16 3.404012e-13 1.480918e-13
## GO:0097193 319/18888 1.305023e-15 1.113837e-12 4.845756e-13
## GO:0071214 334/18888 2.794318e-15 1.589967e-12 6.917162e-13
## GO:0104004 334/18888 2.794318e-15 1.589967e-12 6.917162e-13
##                                                                                                     geneID
## GO:0009411              BCL2/BAK1/MYC/CASP3/TP53/PARP1/CCND1/CDKN1A/AKT1/PIK3R1/MSH6/PRKAA1/BAX/CASP9/PCNA
## GO:0010332                                      BCL2/BAK1/MYC/TP53/YAP1/PARP1/CDKN1A/BCL2L1/PRKAA1/BAX/ATM
## GO:0051402 RB1/ERBB3/FOXO3/BCL2/AXL/CASP3/BCL2L11/TP53/PARP1/XIAP/CTNNB1/PIK3CA/CCND1/BCL2L1/BAX/CASP9/ATM
## GO:0097193 BCL2/BAK1/MYC/CASP3/BCL2L11/TP53/PARP1/CTNNB1/PDK1/CDKN1A/AKT1/PIK3R1/BCL2L1/MSH6/BAX/CASP9/ATM
## GO:0071214 IGF1R/BAK1/MYC/CASP3/TP53/YAP1/PARP1/PIK3CA/MAPK3/CDKN1A/CHEK1/PIK3R1/BCL2L1/BAX/CASP9/ATM/PCNA
## GO:0104004 IGF1R/BAK1/MYC/CASP3/TP53/YAP1/PARP1/PIK3CA/MAPK3/CDKN1A/CHEK1/PIK3R1/BCL2L1/BAX/CASP9/ATM/PCNA
##            Count
## GO:0009411    15
## GO:0010332    11
## GO:0051402    17
## GO:0097193    17
## GO:0071214    17
## GO:0104004    17
##                    ID
## GO:0097136 GO:0097136
## GO:1902911 GO:1902911
## GO:0005741 GO:0005741
## GO:0061695 GO:0061695
## GO:0031968 GO:0031968
## GO:0019867 GO:0019867
##                                                               Description
## GO:0097136                                   Bcl-2 family protein complex
## GO:1902911                                         protein kinase complex
## GO:0005741                                   mitochondrial outer membrane
## GO:0061695 transferase complex, transferring phosphorus-containing groups
## GO:0031968                                       organelle outer membrane
## GO:0019867                                                 outer membrane
##            GeneRatio   BgRatio       pvalue     p.adjust       qvalue
## GO:0097136      5/69  10/19894 1.076634e-10 2.820781e-08 1.631950e-08
## GO:1902911      7/69 150/19894 8.783710e-07 7.475206e-05 4.324747e-05
## GO:0005741      8/69 219/19894 8.913377e-07 7.475206e-05 4.324747e-05
## GO:0061695      9/69 308/19894 1.141253e-06 7.475206e-05 4.324747e-05
## GO:0031968      8/69 248/19894 2.260908e-06 1.048005e-04 6.063188e-05
## GO:0019867      8/69 250/19894 2.400012e-06 1.048005e-04 6.063188e-05
##                                                           geneID Count
## GO:0097136                          BCL2/BAK1/BCL2L11/BCL2L1/BAX     5
## GO:1902911               RB1/IGF1R/CCND1/CDKN1A/IRS1/PRKAA1/PCNA     7
## GO:0005741           FOXO3/BCL2/BAK1/BCL2L11/RAF1/BCL2L1/BAX/PGR     8
## GO:0061695 RB1/IGF1R/PIK3CA/CCND1/CDKN1A/IRS1/PIK3R1/PRKAA1/PCNA     9
## GO:0031968           FOXO3/BCL2/BAK1/BCL2L11/RAF1/BCL2L1/BAX/PGR     8
## GO:0019867           FOXO3/BCL2/BAK1/BCL2L11/RAF1/BCL2L1/BAX/PGR     8
barplot(ego_MF[[1]], title = "enrichGO, Molecular Function, \n 3-Fold CV, alpha = 0.5, MSE")

barplot(ego_MF[[2]], title = "enrichGO, Molecular Function, \n 3-Fold CV, alpha = 0.5, AUC")

barplot(ego_MF[[3]], title = "enrichGO, Molecular Function, \n 3-Fold CV, alpha = 1, MSE")

barplot(ego_MF[[4]], title = "enrichGO, Molecular Function, \n 5-Fold CV, alpha = 0.2, MSE")

barplot(ego_MF[[5]], title = "enrichGO, Molecular Function, \n 5-Fold CV, alpha = 1, MSE")

barplot(ego_MF[[6]], title = "enrichGO, Molecular Function, \n 10-Fold CV, alpha = 0.2, MSE")

barplot(ego_MF[[7]], title = "enrichGO, Molecular Function, \n 10-Fold CV, alpha = 0.5, Deviance")

barplot(ego_BP[[1]], title = "enrichGO, Biological Process, \n 3-Fold CV, alpha = 0.5, MSE")

barplot(ego_BP[[2]], title = "enrichGO, Biological Process, \n 3-Fold CV, alpha = 0.5, AUC")

barplot(ego_BP[[3]], title = "enrichGO, Biological Process, \n 3-Fold CV, alpha = 1, MSE")

barplot(ego_BP[[4]], title = "enrichGO, Biological Process, \n 5-Fold CV, alpha = 0.2, MSE")

barplot(ego_BP[[5]], title = "enrichGO, Biological Process, \n 5-Fold CV, alpha = 1, MSE")

barplot(ego_BP[[6]], title = "enrichGO, Biological Process, \n 10-Fold CV, alpha = 0.2, MSE")

barplot(ego_BP[[7]], title = "enrichGO, Biological Process, \n 10-Fold CV, alpha = 0.5, Deviance")

barplot(ego_CC[[1]], title = "enrichGO, Cellular Component, \n 3-Fold CV, alpha = 0.5, MSE")

barplot(ego_CC[[2]], title = "enrichGO, Cellular Component, \n 3-Fold CV, alpha = 0.5, AUC")

barplot(ego_CC[[3]], title = "enrichGO, Cellular Component, \n 3-Fold CV, alpha = 1, MSE")

barplot(ego_CC[[4]], title = "enrichGO, Cellular Component, \n 5-Fold CV, alpha = 0.2, MSE")

barplot(ego_CC[[5]], title = "enrichGO, Cellular Component, \n 5-Fold CV, alpha = 1, MSE")

barplot(ego_CC[[6]], title = "enrichGO, Cellular Component, \n 10-Fold CV, alpha = 0.2, MSE")

barplot(ego_CC[[7]], title = "enrichGO, Cellular Component, \n 10-Fold CV, alpha = 0.5, Deviance")

DAG plots for ego

goplot(ego_MF[[1]]) + labs(title = "enrichGO, Molecular Function, \n 3-Fold CV, alpha = 0.5, MSE")

goplot(ego_MF[[2]]) + labs(title = "enrichGO, Molecular Function, \n 3-Fold CV, alpha = 0.5, AUC")

goplot(ego_MF[[3]]) + labs(title = "enrichGO, Molecular Function, \n 3-Fold CV, alpha = 1, MSE")

goplot(ego_MF[[4]]) + labs(title = "enrichGO, Molecular Function, \n 5-Fold CV, alpha = 0.2, MSE")

goplot(ego_MF[[5]]) + labs(title = "enrichGO, Molecular Function, \n 5-Fold CV, alpha = 1, MSE")

goplot(ego_MF[[6]]) + labs(title = "enrichGO, Molecular Function, \n 10-Fold CV, alpha = 0.2, MSE")

goplot(ego_MF[[7]]) + labs(title = "enrichGO, Molecular Function, \n 10-Fold CV, alpha = 0.5, Deviance")

goplot(ego_BP[[1]]) + labs(title = "enrichGO, Biological Process, \n 3-Fold CV, alpha = 0.5, MSE")

goplot(ego_BP[[2]]) + labs(title = "enrichGO, Biological Process, \n 3-Fold CV, alpha = 0.5, AUC")
## Warning: ggrepel: 8 unlabeled data points (too many overlaps). Consider
## increasing max.overlaps

goplot(ego_BP[[3]]) + labs(title = "enrichGO, Biological Process, \n 3-Fold CV, alpha = 1, MSE")
## Warning: ggrepel: 4 unlabeled data points (too many overlaps). Consider
## increasing max.overlaps

goplot(ego_BP[[4]]) + labs(title = "enrichGO, Biological Process, \n 5-Fold CV, alpha = 0.2, MSE")

goplot(ego_BP[[5]]) + labs(title = "enrichGO, Biological Process, \n 5-Fold CV, alpha = 1, MSE")
## Warning: ggrepel: 9 unlabeled data points (too many overlaps). Consider
## increasing max.overlaps

goplot(ego_BP[[6]]) + labs(title = "enrichGO, Biological Process, \n 10-Fold CV, alpha = 0.2, MSE")

goplot(ego_BP[[7]]) + labs(title = "enrichGO, Biological Process, \n 10-Fold CV, alpha = 0.5, Deviance")

goplot(ego_CC[[1]]) + labs(title = "enrichGO, Cellular Component, \n 3-Fold CV, alpha = 0.5, MSE")

goplot(ego_CC[[2]]) + labs(title = "enrichGO, Cellular Component, \n 3-Fold CV, alpha = 0.5, AUC")

goplot(ego_CC[[3]]) + labs(title = "enrichGO, Cellular Component, \n 3-Fold CV, alpha = 1, MSE")

goplot(ego_CC[[4]]) + labs(title = "enrichGO, Cellular Component, \n 5-Fold CV, alpha = 0.2, MSE")

goplot(ego_CC[[5]]) + labs(title = "enrichGO, Cellular Component, \n 5-Fold CV, alpha = 1, MSE")

goplot(ego_CC[[6]]) + labs(title = "enrichGO, Cellular Component, \n 10-Fold CV, alpha = 0.2, MSE")

goplot(ego_CC[[7]]) + labs(title = "enrichGO, Cellular Component, \n 10-Fold CV, alpha = 0.5, Deviance")

3. Export Pathway Analysis result to data

pathway = list("ggo_MF" = ggo_MF,
               "ggo_BP" = ggo_BP,
               "ggo_CC" = ggo_CC,
               "ego_MF" = ego_MF,
               "ego_BP" = ego_BP,
               "ego_CC" = ego_CC)

saveRDS(pathway, file = "data/out_pathway/pathways_glmnet.rds")